RetrogeneDB ID: | retro_sita_4 | ||
Retrocopy location | Organism: | Foxtail millet (Setaria italica) | |
| Coordinates: | 5:31269708..31272594(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | Si005170m.g | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | Si000029m.g | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sita_4
ATGAGGAATCAGCTGAAAGATACAATGGACAAATGCAACCTCCTATCATCAGAAGTTGAGAAGGCCCAACAGGCTGAGAA
AGAAGTGCATGCCTTGTTGGAAGAAAACCAGAAGCTGAAGAATGATAACTTGATGCTGTTGGTTGAGCATGATAACCTGA
AAGCACTTCATCAGAATTTAGATGTTGAGTGCTTTCAACTGAAGGCAGCCATTGCAGAAATCACCGCTGAAAATGAATCC
TTGATCACAGAAAATCATTCAGCTGAAAGAAAACTCCAGCAACTGGGGTTGGAGATAGATGGCCTGAAAGTCGAGGCCGC
AGAGTTAATGAACAATCTAGACAAGGAGCGTAATAATGCAGCAGAAGAAAAAGAAAGACTAGTATCAGAAAATTCCATAT
ACTTGAATGAGATAGAGAAGGCACAGTCTAGTATTAAAGATCTAGAAAAGGAACTGGAATCAACAAGAAATGTTATGAAT
AGTAATATGGCCGAGCTACAGGAGGAGAAGGATTCGGCCATGTCAGAGGTAGAGCAGCTAGAGGCTTCTTTGATGAATCT
TAAGACTGAGCTAGCACAACAACTTGAGAGGATTTCAGATATGCAGAAGACTACTGAAGAACTGGAGCTGGCAAATTCTA
ACATGCATAATGAAATTGTAGAAGTAAAAGGACAAAAAAATGAAGCTGCTGCTTCTGTTATTAATCTTGAAAGCAATTTA
GAACAACAAGTTGAACAAATTTCTGTTCTGCAGCTTTCTAATGAAGACCTACAAAATAGTAACTCCAACCTGAAGATGCA
ACTGGAAGAGGCGAAGGTTAGTCACCATGCTGAAATTTTAGCATTACAAGATGAAAGGAACAAAATAATTTCAGATCTGC
AGCAGTCTGAGGCTTCTATCAAGAATCTTAGAATTGAATTGGAGCAAGGAAAAGAGCAAATCTCAAAAATGAATCTAGCT
AATGAAGATCTGAAGAACAACATTGCTATATTGGACAAGCAATTGGAGGAGGTCAGGAGCAGTTTGCATGCTGAAATTGC
ACAACTACAAGCAGAGAAGGGCATAGTTCTATCAGAGTTACAGGTGTCTCAGGCTTCTGTCAGAAACTTGGAGAGTGTGC
TAAAAAAGCAAAGTGAGAAGATTTCAACTCTGGATCAAGCTAATGATCAGTTACAGAAAAACATATGTACCTTGACTGAG
CAATCAGAACAAACCAAGGCTGAGCTGCAGAAGGAGGTTGAGGCAACACAAGAAGAGAAGGATACAACACTAACACAACT
AAAGCAGTCACAGACTTCAGTACAAAATCTTGAGAATGAGGTGACACGACTGAAAGAGGATCTTTCAGTTCAGCTAGAAA
GCAATTCCACCTTGGACAAGCAGTTGGAAGAAGTCAGGAGCAGTACGCATGCTGAAATTGCAGAACTACGTGCAGAGAAG
GACGCAACGCTATTGGAGTTACAGACGTCTCAGGCTTCTGTCAGAAATCTTGAGATTGCCCTTCAAACCCAAAACGAGAA
CATTTCAACTCTACAGCAAGCTAATGATGAGTCACAGAAGATCATTTGTACTTTGACCGAGCAATCAGAACAAGCCAAGG
CTGAGCTGCAGCAGGAGGTTAAGGCTACACAAGAAGAGAAGGATGCAGTGCTAACAAAGCTGAAGCAATCAGAGGATTCA
GTACAAAATCTTGCGAATGAGGTGACACAGCTGAAAGATGAACTTTCAGTTCAGCTGGAAAATAATTCTACCTTGGAAAA
GCAGTTGGAAGAGGCAATACTAAAAGTATCTAACCTACATGAGAATCTCGAGAAGGCTCAGGCTGAAGCAGCTTGTCAAA
TTGATGACATGAGTACAAAAACAAAAGATCTGGAGAAGACAATCGCTCTATTGTCTTATCAAAAGACCAAGTTGGAGGAG
GATCTAAAAATTATGATTGAAGCATGCACAGTAAACATGTCATTTATGACGGAATTTGAAGATAGAGTTACACAAAAAAA
TTCAGATCATGAGGCTGGACTTGTGGTTCTCCGCCAGAGCCTGAAAGGGGTTGCTAGCAGCTGTCAGAGGCTTCAGTATG
CATATGATGAGGTGTCCTCGAGGGTCTCCCAGCTCGAGATACTTAAGAGGCTTCAGATTGAGCAGATAGGTCAACTAGAG
GAGAAACACACAGAAACTTTGGAGAAACATCGACTTCTGGAAGAGGAAAATTTATCTGCAAATAAGGAGAACACAAAGCT
ACAAAAGGATGTCCAAGACCTTGAAGTTCAACTCCAGCTAGCCAAGCAGAAGCTTAAAGTTACCGAGGCAGAAAGCAAAT
GCAAAGAAGACAGCTACGCAATGGCAGTGGAGACATCACAGGCAGAGATCCATCATCTTGAACAACTGGTAAAACAATTT
TCTGGGAGAGTCAACTTGCTGGAAGAAACTCTCATGCAAGTAAAAGGACATGCCGAATCAGGGGTCTCTGAATTGGCTGA
CAAATTGGACGAGCTAGAACCACTCTTGTGTCAGAGTTTTGCACTCTTCGTTGATCGTTCATCTGCATGTGGTGAAGAGC
TTAATGTCCTGAGGAAGAAGCTACATGATCATCTTGATGAACAGAAGGAGCTTGTCAAGGAGAATGATGAGATGGCTGTC
AGGTTGAGAGAGAAAGAAAAATTGGTGTCAGAAATGGTGAAGAACACAGCTGATGCAGAAGCGAAGATGGTCCAGCTCGA
GAAGACGGTGGCAGAGAAAGAAGAAGAGCTAGCAGCTAGAGTGCAGGAGAAGAGAGAAGCCATTAAGCAGCTGAGCGACG
CGATTGTTTACCACAAGAACTATAGCGATGATCTGGTGCGCTACATCCGCAGTCACAATCGCCCTCGCCTCCCATTCTGT
CTGTAA
ORF - retro_sita_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.21 % |
| Parental protein coverage: | 50.88 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NLHNEIVELHGQKNEAADSVINLESKLEQQ----VQEISNLQKANKDLKAAKTDLYNEITALQEEKNAAL |
| NL....VE...Q.............KL.........E..NL......L......L...I.....E..... | |
| Retrocopy | NLLSSEVEKAQQAEKEVHALLEENQKLKNDNLMLLVEHDNLKALHQNLDVECFQLKAAIAEITAENESLI |
| Parental | AQLQESEANIKKLQSDLRVEQISDLQLANEDLQKSNSKLKMQLEEAKFSHQAEILALQDEKNKIISDLQQ |
| ......E.....L.............L.N..L.K.........E...................I...... | |
| Retrocopy | TENHSAERKLQQLGLEIDGLKVEAAELMN-NLDKERNNAAEEKERLVSENSIYLNEIEKAQSSIKDLEKE |
| Parental | SEASIKILVSNIAELQKDNDSAMSEIEQLEASLMNLKTELAQQLERISDMQKTNEGLELANSNLHNEIVE |
| .E.......SN.AELQ...DSAMSE.EQLEASLMNLKTELAQQLERISDMQKT.E.LELANSN.HNEIVE | |
| Retrocopy | LESTRNVMNSNMAELQEEKDSAMSEVEQLEASLMNLKTELAQQLERISDMQKTTEELELANSNMHNEIVE |
| Parental | LQGQKNEPATSVINLESKLEQQVQEISKLQEANKDLEAGKTDLYNEVMALQAEKNAALAQLQQSEANIKE |
| ..GQKNE.A.SVINLES.LEQQV..IS.LQ..N.DL......L............A....LQ........ | |
| Retrocopy | VKGQKNEAAASVINLESNLEQQVEQISVLQLSNEDLQNSNSNLKMQLEEAKVSHHAEILALQDER---NK |
| Parental | LQSDMVQQQNQILHFQRENEEMQSTNSRLHKQLEEIRTNLQDEIIVLQGEKEEAINSLHQSNDSVKTLR- |
| ..SD..Q....I.....E.E......S......E....N....I..L....EE...SLH........... | |
| Retrocopy | IISDLQQSEASIKNLRIELEQGKEQISKMNLANEDLKNN----IAILDKQLEEVRSSLHAEIAQLQAEKG |
| Parental | -VQLEQQVEQISVLQLANEDLQNINSRLKMQLEEAKCSHQAEILALQDE----KNKIISDLQQSEASIKN |
| .V..E.QV.Q.SV..L..E......S.....L..A....Q..I..L.......K................ | |
| Retrocopy | IVLSELQVSQASVRNL--ESVLKKQSEKISTLDQANDQLQKNICTLTEQSEQTKAELQKEVEATQEEKDT |
| Parental | LRIELKQGKEQI----SEMNLSNEDLTNNI---AILNKQLEEVRSSLHAEIAQLQAEKGIVLSELQVSQA |
| ....LKQ..........E.....EDL.........L.KQLEEVRSS.HAEIA.L.AEK...L.ELQ.SQA | |
| Retrocopy | TLTQLKQSQTSVQNLENEVTRLKEDLSVQLESNSTLDKQLEEVRSSTHAEIAELRAEKDATLLELQTSQA |
| Parental | SVRNLESVLEKQSEKISTLDQANDQLQKNICTLTEQSEQTKAELQKEVEATQEEKDTALTQLKQSQTSVQ |
| SVRNLE..L..Q.E.ISTL.QAND..QK.ICTLTEQSEQ.KAELQ.EV.ATQEEKD..LT.LKQS..SVQ | |
| Retrocopy | SVRNLEIALQTQNENISTLQQANDESQKIICTLTEQSEQAKAELQQEVKATQEEKDAVLTKLKQSEDSVQ |
| Parental | NLENEVTQLKDELSVQLENNSTLEKQLEEAILKVSNLHENLEKAQAEAACQIDDMSTKTKDLEKTIDLLS |
| NL.NEVTQLKDELSVQLENNSTLEKQLEEAILKVSNLHENLEKAQAEAACQIDDMSTKTKDLEKTI.LLS | |
| Retrocopy | NLANEVTQLKDELSVQLENNSTLEKQLEEAILKVSNLHENLEKAQAEAACQIDDMSTKTKDLEKTIALLS |
| Parental | CRKTKLEEDLKIMIKACIVNMSFMTEFEDRVTQKISDYEAGLVALHQSLKGVTSSCQRLQYAYDEVSSRV |
| ..KTKLEEDLKIMI.AC.VNMSFMTEFEDRVTQK.SD.EAGLV.L.QSLKGV.SSCQRLQYAYDEVSSRV | |
| Retrocopy | YQKTKLEEDLKIMIEACTVNMSFMTEFEDRVTQKNSDHEAGLVVLRQSLKGVASSCQRLQYAYDEVSSRV |
| Parental | SQLEILKRSQIEEIGQLEVKHTETLEKHRLLEEENLSANKVNTKLQKHVQDLEVQLQLAKQKLKVTEAES |
| SQLEILKR.QIE.IGQLE.KHTETLEKHRLLEEENLSANK.NTKLQK.VQDLEVQLQLAKQKLKVTEAES | |
| Retrocopy | SQLEILKRLQIEQIGQLEEKHTETLEKHRLLEEENLSANKENTKLQKDVQDLEVQLQLAKQKLKVTEAES |
| Parental | KCKEDSYAMAVETSQAEIHRLEQLVKQFSGRVSLLEETLMQVKGHAVSGVKVLRKKLHD |
| KCKEDSYAMAVETSQAEIH.LEQLVKQFSGRV.LLEETLMQVKGHA.SGV..L..KL.. | |
| Retrocopy | KCKEDSYAMAVETSQAEIHHLEQLVKQFSGRVNLLEETLMQVKGHAESGVSELADKLDE |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Setaria italica was not studied using RNA-Seq expression data.
Setaria italica was not studied using ChIP-Seq data.
Setaria italica was not studied using EST data.
Setaria italica was not studied using FANTOM5 data.
retro_sita_4 was not experimentally validated.
Retrocopy orthology:
Setaria italica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Setaria italica | Si000029m.g | 1 retrocopy |
retro_sita_4 ,
|