RetrogeneDB ID: | retro_alyr_9 | ||
Retrocopy location | Organism: | Lyre-leaved rock-cress (Arabidopsis lyrata) | |
| Coordinates: | 3:11969176..11971390(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | scaffold_303017.1 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | Al_scaffold_0001_2882 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_alyr_9
ATGATTAATTCATCCTGTAGCAGCTCCTCCACAAACAAAACCCTATCGTCCCCGGCAAGGAACCTAACTCTGCAAAGTCG
GATCGAAGCGGCTTTAGAAAAGAAAGCAGAAATCACTACGGTGCTTGAGCAATGGCGACAACAACAAGAACAAGGGAAGC
AATTAAACCCTTCGTTGGTGAGAGGTGTCGTCGAGAACCTACGCGATTCCCAGCGATGTCGCGAAGCCCTAGAGGTATCA
AATTGGATGATTGTACAAAAGATCTGCAATCTCATCCCTGAAGATTTCACTACTCGATTTCATCTGATTGAGAACGTATT
TGGATTGGAAGAAGCAGGGAATTTCGTCGAGAGCATCCCGGAGAATTTAAGAAACGAATCTATCTACAATTCTCTTCTAA
GCAGCTACGTAAGACGAAATGATTTGGATAAAGCCGAATCTACTTTCAAGAAGATGAGGGAGCTAGGGTTGCTATTGAGA
GCTTCACCGTATAACTCGATGACTTCACTCTACAGGCGTATCCCTCACGGTAACCGGTGTAAGGTCGATGAGATTCTGCG
AGAGATGAAGGAGAGCAACATTAAGCTTGATAGAGACACCGTGAACAATGCTTTGCGAGTATACGCTGATGTAACTCACA
TAGCGACAATGGAGAAGTTTCTTGCTGAATGGGAAGGGAATACACCGCTTGACTGGCTCACAAGACTTGACATGGCTAAG
GCTTATCTCAGAAGTGGTTTTAAGGGAAAGGCTAAAGAGATGCTTCGTAGAACAGAGGAATTGAGGGATCCAAAGTCCTA
TGAGGAACTCATGAGGCTATATGGTGAAGCAGGAGGGAGAAAGGACGTTTACCGTGTATGGGACTTGTACAAGAAGTTAA
GTAAGAAAGACAACGAAGGATTCCGAGCTTTGATTGGTTCACTATTGAAGCTTGATGATATAAACGGAGCAGAGGAGTTC
TACTACAAAGAGTGGGAGTGCTCGGGACTTCCGTTCGATGTCCGAATCCCGACTATGTTGGTGTCTAGTTACCGCGAAAA
GGGAATGGTGGAGAAGGCAGATAAACTAATAAAGGAGATTATGAAGAATGAAGAATCTGTTAAACCAATCACTCCGTTGT
TGGAGTCATTGGAAAGAAAAGGGAATGTAGTGAAGCCTTCGGAGTTAAGAGATCTCATCAAGAATCTCTGTGACTCAAAT
CAATTCTATAAAGCACTTGAGGCATCAAAATGGATGAGTACAAAAACATCTTTCAATCTTTTCCCTCAAGATTATGCAGC
TAGGCTTCATATGATTGAAAACGTGTTAGGTTTTGAGGAAGCAGAGAAGTTTTTCGAAAGAAGCATTCCGGAGAACATGA
AGGATGACTATGTCTACGGTACACTCTTAAGCTGTTACGCGAAATCTCACAAAACTTTGGATAAAGCCGAGGCCATTTTC
GAGAAGATGGGAGACCTCGGTTTCCTCTCGAAACCTTCTCCATTCAACTCGATGATATCTCTTTACAGTCAGCTAGGAAA
ACGAGAGAAGGTGGAAAATCTTATATCGAAGATGAAATGTATGAACATAGAGCCGGATAGTCTCACGATGAACAACGTTT
TGAGAATGTACGCAGATGAAACCGACATAAAGACAATGGACAAGTATAAAAGAGAGTGGATTAATGCTGAGAAAAACACC
AAGCTTGAGATGAGGACCATGGTTGCAATGGCGAATGCTTACGAGAGAGCCGGTCTACTACTAAAGGCGATTGAGATAAC
AAGGAGTAAAAATGAAGTTCACCGTCTATGGAATGAGTACAAGGAGAAGGAAAAGAGAAATTATAAAATAGATGACGCCA
ATCTATGTAAGTGTAGAAGTGCGGTTGGTGATGAAGAATATCAAAGTGTGATTAGCTCTTTGTTGAAGCTAGACGATTTA
AAAGGAGCAGAGGAGATATATGGAGAGTGGGAACCAGAAGGACCCGAGTTCAATACTCGAATACCGTGTTTGATAATCTC
TCGTTACTGCAAGGAAGGCGATGAAGTGAAGGTAAGGGAAGTAGTGTACTCGAGTATAAAGAAGCGGAAGCTAATGCAGT
TTGAGAGTTTCAAGGAAGATGTGTACGTCTTTGGTGCCATATGTATAGTGTGTGTGGGTTTTGTGGGCGTGCTATTAATG
ATTATAACGAACCCCTTGCTCTTTTTTTTTCTCCTAATTCATTTGTCTCGTTAA
ORF - retro_alyr_9 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.8 % |
| Parental protein coverage: | 73.46 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TLNHRITDALHRNAQIIPVLEQWRQ---QGNQVNPSHVRVIIKKLRDSDQSLQALQVSEWMSKEKICNLI |
| TL..RI..AL...A.I..VLEQWRQ...QG.Q.NPS.VR.....LRDS.....AL.VS.WM...KICNLI | |
| Retrocopy | TLQSRIEAALEKKAEITTVLEQWRQQQEQGKQLNPSLVRGVVENLRDSQRCREALEVSNWMIVQKICNLI |
| Parental | PEDFAARLHLIENVVGLEEAEKFFESIPKNARDDSVYTTLLNWYARSDKTLCKAEATFQKMRELGLLSRP |
| PEDF..R.HLIENV.GLEEA..F.ESIP.N.R..S.Y..LL..Y.R....L.KAE.TF.KMRELGLL.R. | |
| Retrocopy | PEDFTTRFHLIENVFGLEEAGNFVESIPENLRNESIYNSLLSSYVRRN-DLDKAESTFKKMRELGLLLRA |
| Parental | SPYNAMMSLY--IALNDREKVEELLREMKDNDVEADSITVNNVLKLYSAVCDVTAMEKFLNKWEGINGIK |
| SPYN.M.SLY..I....R.KV.E.LREMK......D..TVNN.L..Y..V.....MEKFL..WEG..... | |
| Retrocopy | SPYNSMTSLYRRIPHGNRCKVDEILREMKESNIKLDRDTVNNALRVYADVTHIATMEKFLAEWEG--NTP |
| Parental | LEWLTTLDMAKAYLRARSNGKAIKMLRLTEELADRKSLKSAYDHLMKLYGEAGNREEVLRIWNLYKMNIG |
| L.WLT.LDMAKAYLR....GKA..MLR.TEEL.D.KS....Y..LM.LYGEAG.R..V.R.W.LYK.... | |
| Retrocopy | LDWLTRLDMAKAYLRSGFKGKAKEMLRRTEELRDPKS----YEELMRLYGEAGGRKDVYRVWDLYK-KLS |
| Parental | QRDNKGYRTVIRSLLKVDDIFGAEEI-YKVWESLSLEFDIRIPTMLASGYRERGMTEKAEKLINSKTIKD |
| ..DN.G.R..I.SLLK.DDI.GAEE..YK.WE...L.FD.RIPTML.S.YRE.GM.EKA.KLI.....K. | |
| Retrocopy | KKDNEGFRALIGSLLKLDDINGAEEFYYKEWECSGLPFDVRIPTMLVSSYREKGMVEKADKLI-KEIMKN |
| Parental | RKMNKPVTPLLE---QWGDQMKPSDLKCLIKNLRDSNQFSKALQVSEWMGEKRVCDLYSEDYAARLYLTE |
| ....KP.TPLLE.....G...KPS.L..LIKNL.DSNQF.KAL..S.WM..K....L...DYAARL...E | |
| Retrocopy | EESVKPITPLLESLERKGNVVKPSELRDLIKNLCDSNQFYKALEASKWMSTKTSFNLFPQDYAARLHMIE |
| Parental | NVLGLEKAEKYFE-NIPENMKDYSVYVALLSSYAKSDKNLENMVEEILREMEENNVDPDSITVNYVLKVY |
| NVLG.E.AEK.FE..IPENMKD..VY..LLS.YAKS.K.L....E.I...M............N.....Y | |
| Retrocopy | NVLGFEEAEKFFERSIPENMKDDYVYGTLLSCYAKSHKTLDK-AEAIFEKMGDLGFLSKPSPFNSMISLY |
| Parental | AAASKVEAME |
| ....K.E..E | |
| Retrocopy | SQLGKREKVE |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Arabidopsis lyrata was not studied using RNA-Seq expression data.
Arabidopsis lyrata was not studied using ChIP-Seq data.
Arabidopsis lyrata was not studied using EST data.
Arabidopsis lyrata was not studied using FANTOM5 data.
retro_alyr_9 was not experimentally validated.
Retrocopy orthology:
Arabidopsis lyrata 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 | |
|---|---|---|---|
| Arabidopsis lyrata | Al_scaffold_0001_2882 | 1 retrocopy |
retro_alyr_9 ,
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