rna-KK1_019894

Transcript Overview


Name	rna-KK1_019894
Unique Name	rna-KK1_019894_Cc_Asha_v1.0
Type	mRNA
Organism	Cajanus cajan (pigeon pea)
Sequence length	1263
Product	hypothetical protein

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
Chr_1-CM003603.1	supercontig	Chr_1-CM003603.1:1605490..1606752 +	Cajanus cajan Asha genome v1.0	n/a
Chr_1-CM003603.1	supercontig	Chr_1-CM003603.1:1605490..1606752 +	Cajanus cajan Asha genome v1.0	n/a

Analyses

This mRNA is derived from or has results from the following analyses


Analysis Name	Date Performed
Cajanus cajan Asha genome v1.0	2019-09-17
BLAST: C. cajan Asha genome v1.0 vs. Swissprot	2019-10-17

Orthologs

Syntenic blocks


Syntentic block	Assembly	Species
cccrR0011	Cicer reticulatum L. PI489777 genome v1	Cicer reticulatum
cccrR0043	Cicer reticulatum L. PI489777 genome v1	Cicer reticulatum
ccpsR022	Pisum sativum Cameor genome v1a	Pisum sativum
ccpsR024	Pisum sativum Cameor genome v1a	Pisum sativum
ccpsR033	Pisum sativum Cameor genome v1a	Pisum sativum
ccccR001	Cajanus cajan Asha genome v1.0	Cajanus cajan
ccpvR0004	Phaseolus vulgaris G19833 genome v2.1	Phaseolus vulgaris
ccpvR0019	Phaseolus vulgaris G19833 genome v2.1	Phaseolus vulgaris
ccvuR0003	Vigna unguiculata L. Walp IT97K-499-35 genome v1.1	Vigna unguiculata
ccvuR0016	Vigna unguiculata L. Walp IT97K-499-35 genome v1.1	Vigna unguiculata
cctifR0008	Vicia faba cv. Tiffany genome v1.0	Vicia faba
cctifR0010	Vicia faba cv. Tiffany genome v1.0	Vicia faba
cctifR0036	Vicia faba cv. Tiffany genome v1.0	Vicia faba
ccvfhR0010	Vicia faba inbred line Hedin/2 genome v1.0	Vicia faba
ccvfhR0039	Vicia faba inbred line Hedin/2 genome v1.0	Vicia faba
ccvrvR0014	Vigna radiata cv. VC1973A genome v6.0	Vigna radiata
ccvrvR0038	Vigna radiata cv. VC1973A genome v6.0	Vigna radiata
ccvssR0010	Vicia sativa cv. Studenica genome v1.0	Vicia sativa
ccvuaR0003	Vigna unguiculata subsp. sesquipedalis line A147 genome v1.0	Vigna unguiculata subsp. sesquipedalis
ccvssR0042	Vicia sativa cv. Studenica genome v1.0	Vicia sativa
ccvuaR0020	Vigna unguiculata subsp. sesquipedalis line A147 genome v1.0	Vigna unguiculata subsp. sesquipedalis
canccL0553	Cicer arietinum CDC Frontier NCBI RefSeq v1	Cicer arietinum
canccL0728	Cicer arietinum CDC Frontier NCBI RefSeq v1	Cicer arietinum
ccccaR0000	Cajanus cajan cv. Asha genome v2.0	Cajanus cajan
ccccaR0054	Cajanus cajan cv. Asha genome v2.0	Cajanus cajan
ccvumR0009	Vigna umbellata FF25 genome v1.0	Vigna umbellata
ccvumR0042	Vigna umbellata FF25 genome v1.0	Vigna umbellata

Orthologs


Gene/Transcript	Assembly	Species
Vfaba.Tiffany.R1.1g090080.1	Vicia faba cv. Tiffany genome v1.0	Vicia faba

Relationships

This mRNA is a part of the following gene feature(s):


Feature Name	Unique Name	Species	Type
gene-KK1_019894	gene-KK1_019894_Cc_Asha_v1.0	Cajanus cajan	gene

The following polypeptide feature(s) derives from this mRNA:


Feature Name	Unique Name	Species	Type
rna-KK1_019894	rna-KK1_019894_Cc_Asha_v1.0-protein	Cajanus cajan	polypeptide
rna-KK1_019894_Cc_Asha_v1.0	rna-KK1_019894_Cc_Asha_v1.0	Cajanus cajan	polypeptide

The following exon feature(s) are a part of this mRNA:


Feature Name	Unique Name	Species	Type
rna-KK1_019894_Cc_Asha_v1.0-exon-Chr_1-CM003603.1_Cc_Asha_v1.0-1571082112:1605490..1606752	rna-KK1_019894_Cc_Asha_v1.0-exon-Chr_1-CM003603.1_Cc_Asha_v1.0-1571082112:1605490..1606752	Cajanus cajan	exon
rna-KK1_019894_Cc_Asha_v1.0-exon-Chr_1-CM003603.1_Cc_Asha_v1.0-1571847872:1605490..1606752	rna-KK1_019894_Cc_Asha_v1.0-exon-Chr_1-CM003603.1_Cc_Asha_v1.0-1571847872:1605490..1606752	Cajanus cajan	exon

The following CDS feature(s) are a part of this mRNA:


Feature Name	Unique Name	Species	Type
rna-KK1_019894_Cc_Asha_v1.0-CDS-Chr_1-CM003603.1_Cc_Asha_v1.0-1571082112:1605490..1606752	rna-KK1_019894_Cc_Asha_v1.0-CDS-Chr_1-CM003603.1_Cc_Asha_v1.0-1571082112:1605490..1606752	Cajanus cajan	CDS
rna-KK1_019894_Cc_Asha_v1.0-CDS-Chr_1-CM003603.1_Cc_Asha_v1.0-1571847872:1605490..1606752	rna-KK1_019894_Cc_Asha_v1.0-CDS-Chr_1-CM003603.1_Cc_Asha_v1.0-1571847872:1605490..1606752	Cajanus cajan	CDS

Homology

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BLAST of rna-KK1_019894 vs. DB:Swiss
Match: POLR1_ARATH (Retrovirus-related Pol polyprotein from transposon RE1 OS=Arabidopsis thaliana OX=3702 GN=RE1 PE=2 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 6.024e-7
Identity = 44/205 (21.46%), Postives = 84/205 (40.98%), Query Frame = 1

Query:  103 LADNNYQQWKHDMIVALETKNKEKFVLGTLAYPPST---------DPLHDAWKRCNKMVMSWLTRSMTPSIKQSVMWMDTAADIWCDLLECFSHGDKFRIVDLQEELQICKQGDSTVSQYYTHLKILWKELTMYRTLLVCTCSSPCNCGLILKIKKERD-DDCVIKFLRGLNDEFSQVRSQIMLMEPMPNLVKSFSLVLQQEREL 687
            L   NY  W   +    +      F+ G+   PP+T         +P +  WKR +K++ S +  +++ S++ +V    TAA IW  L + +++     +  L+ +L+   +G  T+  Y   L   + +L +                    + K  D D+ V + L  L +E+  V  QI   +  P L +    +L  E ++
Sbjct:   26 LTSTNYLMWSRQVHALFDGYELAGFLDGSTTMPPATIGTDAAPRVNPDYTRWKRQDKLIYSAVLGAISMSVQPAVSRATTAAQIWETLRKIYANPSYGHVTQLRTQLKQWTKGTKTIDDYMQGLVTRFDQLAL--------------------LGKPMDHDEQVERVLENLPEEYKPVIDQIAAKDTPPTLTEIHERLLNHESKI 210

The following BLAST results are available for this feature:

BLAST of rna-KK1_019894 vs. DB:Swiss

BLAST of rna-KK1_019894 vs. DB:Swiss
Analysis Date: 2019-10-17 (BLAST: C. cajan Asha genome v1.0 vs. Swissprot)
Total hits: 1

Position :

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Match Name	E-value	Identity	Description
POLR1_ARATH	6.024e-7	21.46	Retrovirus-related Pol polyprotein from transposon...	[more]

InterPro

Analysis Name: Cajanus cajan Asha genome v1.0
Date Performed: 2019-09-17

Position :

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IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR029472	Retrotransposon Copia-like, N-terminal	PFAM	PF14244	Retrotran_gag_3	coord: 21..67 e-value: 7.2E-10 score: 38.5
None	No IPR available	PFAM	PF14223	Retrotran_gag_2	coord: 77..218 e-value: 3.1E-7 score: 30.1
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 245..283
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 245..281
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 309..334

Sequences

The following sequences are available for this feature:

mRNA sequence
protein sequence
mRNA from alignment at Chr_1-CM003603.1:1605490..1606752+
coding sequence from alignment at Chr_1-CM003603.1:1605490..1606752+

mRNA sequence

>rna-KK1_019894_Cc_Asha_v1.0 ID=rna-KK1_019894_Cc_Asha_v1.0; Name=rna-KK1_019894; organism=Cajanus cajan; type=mRNA; length=1263bp
ATGGAAAAATCTGACAACCCTTCTGATCACCTCGTAAATCCAGCAAATCC
CCTTTTTCTACATCCAGGAGAAAACCCTGCACTCGTTCTCGTCACTCCTT
TGCTCGCTGATAACAACTATCAACAATGGAAACATGACATGATTGTGGCT
CTCGAGACAAAGAACAAAGAGAAATTCGTTCTTGGCACTCTTGCTTATCC
TCCTTCCACCGATCCTCTACATGACGCTTGGAAACGATGCAACAAGATGG
TGATGTCGTGGCTCACACGATCCATGACACCTTCCATCAAACAATCGGTT
ATGTGGATGGACACGGCTGCTGACATTTGGTGCGATCTTCTTGAGTGTTT
CTCTCATGGTGACAAATTCCGCATTGTTGATCTACAAGAGGAGCTTCAAA
TCTGCAAGCAAGGTGATTCCACTGTATCACAGTATTATACTCATCTGAAA
ATTCTTTGGAAAGAGCTTACGATGTATCGTACGCTTCTTGTTTGTACCTG
TTCCTCTCCATGTAATTGTGGTTTAATTCTCAAAATCAAAAAAGAACGAG
ATGATGATTGTGTTATCAAGTTTCTTCGTGGCCTTAATGATGAATTCTCT
CAAGTCCGTTCTCAAATCATGCTCATGGAACCTATGCCGAATCTTGTGAA
ATCTTTCTCCCTAGTTCTTCAACAAGAACGTGAGTTAAATGGTTCTTTCT
CTCATAATTCACAAGAGTCAGTTGCTAACATCAATTTTCAAGATAATTCC
AACAAAAACTCTTTCACAAACCGTGGAGGTTTCTCAAATTCTCGAGGCAG
AGGTCGTTCAAATAGATCCGCTGGACGCAACAATAAGTATTGTGATCATT
GCCAACGAACAAATCACACTTCTGAAACTTGTTGGATCAAACATGGACTT
CCAGTAGGTTACAAGAACAGTTTCAAGAATAATTCGAGTTCTTCTAAGCC
TTCTGCTAGTATTGCTGAAAGTGAATCTTCTATTGTCACTGAACCTTCTG
TTGTGGAATCTGACAAGCCAAGTGCTCAATTTGGTTTCTCTAAGGATCAA
TATCAAACCATACTTGCCTTGTTATCACAATCACAAAAAGCCTCTCCTCC
AGTAACAAGTGTCCATCAATGCACTGTTAATTCCTCAGGTTCTGTACCTT
CCTCTTTCTCTTGGATACTGGATAGTGGTGCTACTGACCACATTTGCCCT
TTCAAATCTGCTTTTAAAACTCTTAAACCAATTTCTCCTATTTCCATTCG
GCTACCTAATTAA

protein sequence of rna-KK1_019894_Cc_Asha_v1.0

>rna-KK1_019894_Cc_Asha_v1.0 ID=rna-KK1_019894_Cc_Asha_v1.0; Name=rna-KK1_019894_Cc_Asha_v1.0; organism=Cajanus cajan; type=polypeptide; length=420bp
MEKSDNPSDHLVNPANPLFLHPGENPALVLVTPLLADNNYQQWKHDMIVA
LETKNKEKFVLGTLAYPPSTDPLHDAWKRCNKMVMSWLTRSMTPSIKQSV
MWMDTAADIWCDLLECFSHGDKFRIVDLQEELQICKQGDSTVSQYYTHLK
ILWKELTMYRTLLVCTCSSPCNCGLILKIKKERDDDCVIKFLRGLNDEFS
QVRSQIMLMEPMPNLVKSFSLVLQQERELNGSFSHNSQESVANINFQDNS
NKNSFTNRGGFSNSRGRGRSNRSAGRNNKYCDHCQRTNHTSETCWIKHGL
PVGYKNSFKNNSSSSKPSASIAESESSIVTEPSVVESDKPSAQFGFSKDQ
YQTILALLSQSQKASPPVTSVHQCTVNSSGSVPSSFSWILDSGATDHICP
FKSAFKTLKPISPISIRLPN

mRNA from alignment at Chr_1-CM003603.1:1605490..1606752+

Legend: polypeptideexonCDS

Hold the cursor over a type above to highlight its positions in the sequence below.

>rna-KK1_019894_Cc_Asha_v1.0 ID=rna-KK1_019894_Cc_Asha_v1.0; Name=rna-KK1_019894; organism=Cajanus cajan; type=mRNA; length=1263bp; location=Sequence derived from: Chr_1-CM003603.1:1605490..1606752+ (Cajanus cajan
ATGGAAAAATCTGACAACCCTTCTGATCACCTCGTAAATCCAGCAAATCC
CCTTTTTCTACATCCAGGAGAAAACCCTGCACTCGTTCTCGTCACTCCTT
TGCTCGCTGATAACAACTATCAACAATGGAAACATGACATGATTGTGGCT
CTCGAGACAAAGAACAAAGAGAAATTCGTTCTTGGCACTCTTGCTTATCC
TCCTTCCACCGATCCTCTACATGACGCTTGGAAACGATGCAACAAGATGG
TGATGTCGTGGCTCACACGATCCATGACACCTTCCATCAAACAATCGGTT
ATGTGGATGGACACGGCTGCTGACATTTGGTGCGATCTTCTTGAGTGTTT
CTCTCATGGTGACAAATTCCGCATTGTTGATCTACAAGAGGAGCTTCAAA
TCTGCAAGCAAGGTGATTCCACTGTATCACAGTATTATACTCATCTGAAA
ATTCTTTGGAAAGAGCTTACGATGTATCGTACGCTTCTTGTTTGTACCTG
TTCCTCTCCATGTAATTGTGGTTTAATTCTCAAAATCAAAAAAGAACGAG
ATGATGATTGTGTTATCAAGTTTCTTCGTGGCCTTAATGATGAATTCTCT
CAAGTCCGTTCTCAAATCATGCTCATGGAACCTATGCCGAATCTTGTGAA
ATCTTTCTCCCTAGTTCTTCAACAAGAACGTGAGTTAAATGGTTCTTTCT
CTCATAATTCACAAGAGTCAGTTGCTAACATCAATTTTCAAGATAATTCC
AACAAAAACTCTTTCACAAACCGTGGAGGTTTCTCAAATTCTCGAGGCAG
AGGTCGTTCAAATAGATCCGCTGGACGCAACAATAAGTATTGTGATCATT
GCCAACGAACAAATCACACTTCTGAAACTTGTTGGATCAAACATGGACTT
CCAGTAGGTTACAAGAACAGTTTCAAGAATAATTCGAGTTCTTCTAAGCC
TTCTGCTAGTATTGCTGAAAGTGAATCTTCTATTGTCACTGAACCTTCTG
TTGTGGAATCTGACAAGCCAAGTGCTCAATTTGGTTTCTCTAAGGATCAA
TATCAAACCATACTTGCCTTGTTATCACAATCACAAAAAGCCTCTCCTCC
AGTAACAAGTGTCCATCAATGCACTGTTAATTCCTCAGGTTCTGtacctt
cctctttctcttggATACTGGATAGTGGTGCTACTGACCACATTTGCCCT
TTCAAATCTGCTTTTAAAACTCTTAAACCAATTTCTCCTATTTCCATTCG
GCTACCTAATTAA

Coding sequence (CDS) from alignment at Chr_1-CM003603.1:1605490..1606752+

>rna-KK1_019894_Cc_Asha_v1.0 ID=rna-KK1_019894_Cc_Asha_v1.0; Name=rna-KK1_019894; organism=Cajanus cajan; type=CDS; length=2526bp; location=Sequence derived from: Chr_1-CM003603.1:1605490..1606752+ (Cajanus cajan
ATGGAAAAATCTGACAACCCTTCTGATCACCTCGTAAATCCAGCAAATCC
CCTTTTTCTACATCCAGGAGAAAACCCTGCACTCGTTCTCGTCACTCCTT
TGCTCGCTGATAACAACTATCAACAATGGAAACATGACATGATTGTGGCT
CTCGAGACAAAGAACAAAGAGAAATTCGTTCTTGGCACTCTTGCTTATCC
TCCTTCCACCGATCCTCTACATGACGCTTGGAAACGATGCAACAAGATGG
TGATGTCGTGGCTCACACGATCCATGACACCTTCCATCAAACAATCGGTT
ATGTGGATGGACACGGCTGCTGACATTTGGTGCGATCTTCTTGAGTGTTT
CTCTCATGGTGACAAATTCCGCATTGTTGATCTACAAGAGGAGCTTCAAA
TCTGCAAGCAAGGTGATTCCACTGTATCACAGTATTATACTCATCTGAAA
ATTCTTTGGAAAGAGCTTACGATGTATCGTACGCTTCTTGTTTGTACCTG
TTCCTCTCCATGTAATTGTGGTTTAATTCTCAAAATCAAAAAAGAACGAG
ATGATGATTGTGTTATCAAGTTTCTTCGTGGCCTTAATGATGAATTCTCT
CAAGTCCGTTCTCAAATCATGCTCATGGAACCTATGCCGAATCTTGTGAA
ATCTTTCTCCCTAGTTCTTCAACAAGAACGTGAGTTAAATGGTTCTTTCT
CTCATAATTCACAAGAGTCAGTTGCTAACATCAATTTTCAAGATAATTCC
AACAAAAACTCTTTCACAAACCGTGGAGGTTTCTCAAATTCTCGAGGCAG
AGGTCGTTCAAATAGATCCGCTGGACGCAACAATAAGTATTGTGATCATT
GCCAACGAACAAATCACACTTCTGAAACTTGTTGGATCAAACATGGACTT
CCAGTAGGTTACAAGAACAGTTTCAAGAATAATTCGAGTTCTTCTAAGCC
TTCTGCTAGTATTGCTGAAAGTGAATCTTCTATTGTCACTGAACCTTCTG
TTGTGGAATCTGACAAGCCAAGTGCTCAATTTGGTTTCTCTAAGGATCAA
TATCAAACCATACTTGCCTTGTTATCACAATCACAAAAAGCCTCTCCTCC
AGTAACAAGTGTCCATCAATGCACTGTTAATTCCTCAGGTTCTGtacctt
cctctttctcttggATACTGGATAGTGGTGCTACTGACCACATTTGCCCT
TTCAAATCTGCTTTTAAAACTCTTAAACCAATTTCTCCTATTTCCATTCG
GCTACCTAATTAAATGGAAAAATCTGACAACCCTTCTGATCACCTCGTAA
ATCCAGCAAATCCCCTTTTTCTACATCCAGGAGAAAACCCTGCACTCGTT
CTCGTCACTCCTTTGCTCGCTGATAACAACTATCAACAATGGAAACATGA
CATGATTGTGGCTCTCGAGACAAAGAACAAAGAGAAATTCGTTCTTGGCA
CTCTTGCTTATCCTCCTTCCACCGATCCTCTACATGACGCTTGGAAACGA
TGCAACAAGATGGTGATGTCGTGGCTCACACGATCCATGACACCTTCCAT
CAAACAATCGGTTATGTGGATGGACACGGCTGCTGACATTTGGTGCGATC
TTCTTGAGTGTTTCTCTCATGGTGACAAATTCCGCATTGTTGATCTACAA
GAGGAGCTTCAAATCTGCAAGCAAGGTGATTCCACTGTATCACAGTATTA
TACTCATCTGAAAATTCTTTGGAAAGAGCTTACGATGTATCGTACGCTTC
TTGTTTGTACCTGTTCCTCTCCATGTAATTGTGGTTTAATTCTCAAAATC
AAAAAAGAACGAGATGATGATTGTGTTATCAAGTTTCTTCGTGGCCTTAA
TGATGAATTCTCTCAAGTCCGTTCTCAAATCATGCTCATGGAACCTATGC
CGAATCTTGTGAAATCTTTCTCCCTAGTTCTTCAACAAGAACGTGAGTTA
AATGGTTCTTTCTCTCATAATTCACAAGAGTCAGTTGCTAACATCAATTT
TCAAGATAATTCCAACAAAAACTCTTTCACAAACCGTGGAGGTTTCTCAA
ATTCTCGAGGCAGAGGTCGTTCAAATAGATCCGCTGGACGCAACAATAAG
TATTGTGATCATTGCCAACGAACAAATCACACTTCTGAAACTTGTTGGAT
CAAACATGGACTTCCAGTAGGTTACAAGAACAGTTTCAAGAATAATTCGA
GTTCTTCTAAGCCTTCTGCTAGTATTGCTGAAAGTGAATCTTCTATTGTC
ACTGAACCTTCTGTTGTGGAATCTGACAAGCCAAGTGCTCAATTTGGTTT
CTCTAAGGATCAATATCAAACCATACTTGCCTTGTTATCACAATCACAAA
AAGCCTCTCCTCCAGTAACAAGTGTCCATCAATGCACTGTTAATTCCTCA
GGTTCTGtaccttcctctttctcttggATACTGGATAGTGGTGCTACTGA
CCACATTTGCCCTTTCAAATCTGCTTTTAAAACTCTTAAACCAATTTCTC
CTATTTCCATTCGGCTACCTAATTAA

Annotated Terms

The following terms have been associated with this mRNA:

Vocabulary: **INTERPRO**
Term	Definition
IPR029472	Copia-like_N

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