RetrogeneDB ID: | retro_sara_299 | ||
Retrocopy location | Organism: | Shrew (Sorex araneus) | |
| Coordinates: | scaffold_153587:3385..5276(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSARG00000002498 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNF40 | ||
| Ensembl ID: | ENSSARG00000009524 | ||
| Aliases: | None | ||
| Description: | ring finger protein 40, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:16867] |
Retrocopy-Parental alignment summary:
>retro_sara_299
AGGTCTCAGACACGCACTAGTGATCTTGGCAGTGAGAACCAACGACTGCAAGACTTGGTCACCCAGCTACACGAGAAGTA
CCACCGCATCTCGTTGGAATACTTCGAGCTCCAGGACAAGGTGACGTCATCCGAAACAAAGGTACGAGAGTTGGAGACCA
CTGTAGAGGACCTGCAGTGGGACACCAAGAAGCTACACAAACGCGAGCAGAAGCTCAATAAGAAACTGGCAGAGGCCTTG
AATCAGCTCGACCCTCGCTACAATGTGTCTGGGACCTCCTCAGGCTTCAACTTCCTGAAGTTTGAGACGCTGAAGGCAGA
GTTGAAAGAAAACCAGGAATTGGCCACCAACCGCCTGGCAGAGCTGGAGAAATTGCAAGCCGAATTCCATGGGGCTGTGG
TGACTAAAGAGCGCCTCAACGTGGCCCTGCTGACCCTTCCCATGGAGATGGTTCGGGAGACAGACGAGTACCAAATGCTG
CAAGCCCAGTTCTCATTTCTCTACAATGAATATCTGCAAGTGAAGACCCAGCTGGATGAGAGCCGGGAGCTGCTGCTGTC
CACCAATAATTCCCCACCAGCTGTACATCCAGCACATGGAGAATAATGAGGTTGGAGTGCAGATAAACCTGCGCACAGAG
GTTTTCCACTTGGAGGATACAGTGGCTCGGGTTCGCAAGGAGTATGAGACGCTGCGCTTGGAGTTTGAACAGAACCAAGC
AGCCAATGAACAGGCAGAGCCCATCAACCGGGAGATGCGTCAACTGACCATTAGCCTCCAAATCCATAACAATCAGCTGA
AGAAAGATGTCCATCGCTACAAGCGGAAGCTGAGAGACATACAGGCTGAGATCAACAAACACCAGGCCCGGGCCAGTGGC
TCTGCCCATTCCATCTCTGGTGTGATCCCCACAGGCGATTCTAGCCTCAGTGCCTCAGCACCAGGAAAAGAAGAGGGTGG
GCCTGGCCCAGTAGGTGCCACAGATAACAGGAAGAAATTGGAGGCCATGCCTGCCACTGCCACTGCTACATCATCTGTGA
AGAAGGAAGAGCTGCCCCCTGCTGAGAAAGACCTCCAGCCTGTCACCCCTGTGCCCCAGGGCCTGTCCTCCCAGCCTCAA
AAAACTCAGGCGGGACCCAGCCGGGACTTTAGGGGGCAGGAAAGGCCCAGCCTGGGAGTCCAGCCGAAAGCACGAGCCCA
CTCACGAGCTGAACGGGAGAAGGCCAAGGTGAAGGAGACCAAGAGGAAGACATCAGAACACCTCAAAGGCCTCCGTGCAG
AGCTCAAGAAAGCCCACGAAAGTCAAAAAGAGATGAAACTGTTGCTGGACATGTACAAATTGGCTCCCAAGGAGCAGCGG
GATAATCAGCAGCTCATGGAAGATGAACGCAAGGTCAAGGCTGAGGTGGATCAACTGCAGGGCCATGTCCAGGAGATGGA
GGAGAAGTATCGCAGGGAGAGTAAGAAGCGCGCATATGAACGAGCCCTGCGGTCCAACTGGCAGGCACAGCAGATCAAAT
ACCTGCGGAGGAAGCTGGGGGCCACCAAGCGTGAGGAAGATGCTTTGGCCTCGGAGATGGAAGTGACAGGCCAGGCCTTT
GAGGAATTGCAGGAGCAGAATCAGCGGCTCAAGCAGCAGTTGCAGGAGAAGGATGAAGCCAACTTTAAGCTGCTGTCAGA
GAGGGGCGAGACCAACGACATCTACAAGCTGCTGTGTGAAGAGAAAAGTGAGCTGGAAGAGCAGGTTTTGAGCCTCCAGT
CCCAAGTGAATGCCCAGCTGTTGACTGTGCAGACAATGGAGCATAATGAGTGGATCTTGCAGGGCTGCCTTGGTAGTGTG
GAGAGGGAATTGATGCTGTGCAACCAGGCTCTGGAGCAAACGAAGACGAAG
ORF - retro_sara_299 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.55 % |
| Parental protein coverage: | 62.8 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RENRRLQDLATQ---LQEKHHRISLEYSELQDKVTSSETKVLEMETTVEDLQWDIEKLRKREQKLNKHLA |
| R...R..DL......LQ.........Y............KV...ET.V..L....E.L.....KL.K... | |
| Retrocopy | RSQTRTSDLGSENQRLQDLVTQLHEKYHRISLEYFELQDKVTSSETKVRELETTVEDLQWDTKKLHKREQ |
| Parental | EALEQLNSGYYVSGSSSGFQGGQITLSMQKFEMLNAELEENQELANSRMAELEKLQAELQGAVRTNERLK |
| .....L..............G........KFE.L.AEL.ENQELA..R.AELEKLQAE..GAV.T.ERL. | |
| Retrocopy | KLNKKLAEALNQLDPRYNVSGTSSGFNFLKFETLKAELKENQELATNRLAELEKLQAEFHGAVVTKERLN |
| Parental | VALRSLPEEVVRETGEYRMLQAQFSLLYNESLQVKTQLDEARGLLLATKNS-HLRHIEHMESDELGLQKK |
| VAL..LP.E.VRET.EY.MLQAQFS.LYNE.LQVKTQLDE.R.LLL.T.NS.H...I.HME..E.G.Q.. | |
| Retrocopy | VALLTLPMEMVRETDEYQMLQAQFSFLYNEYLQVKTQLDESRELLLSTNNS>HQLYIQHMENNEVGVQIN |
| Parental | LRTEVIQLEDTLAQVRKEYEMLRIEFEQNLAANEQAGPINREMRHLISSLQNHNHQLKGDAQRYKRKLRE |
| LRTEV..LEDT.A.VRKEYE.LR.EFEQN.AANEQA.PINREMR.L..SLQ.HN.QLK.D..RYKRKLR. | |
| Retrocopy | LRTEVFHLEDTVARVRKEYETLRLEFEQNQAANEQAEPINREMRQLTISLQIHNNQLKKDVHRYKRKLRD |
| Parental | VQAEIGKLRAQASGSAHSVPNVVPPDDSALSTPTPGKEEGGPSPVGATDNRKELAAMPPVATATSSVKKE |
| .QAEI.K..A.ASGSAHS...V.P..DS.LS...PGKEEGGP.PVGATDNRK.L.AMP..ATATSSVKKE | |
| Retrocopy | IQAEINKHQARASGSAHSISGVIPTGDSSLSASAPGKEEGGPGPVGATDNRKKLEAMPATATATSSVKKE |
| Parental | ELPPPEEDPQAVTPGPQGPSSRPREPEARPKRELREREGPSLGAPPAVPALSRADREKAKMEEAKRKESE |
| ELPP.E.D.Q.VTP.PQG.SS.P....A.P.R..R..E.PSLG..P...A.SRA.REKAK..E.KRK.SE | |
| Retrocopy | ELPPAEKDLQPVTPVPQGLSSQPQKTQAGPSRDFRGQERPSLGVQPKARAHSRAEREKAKVKETKRKTSE |
| Parental | LLKGLRAELKKAQESQKEMKLLLDMYKSAPKEQRDKVQLMAAERKAKAEVDELRGRIRELEERDRRESKK |
| .LKGLRAELKKA.ESQKEMKLLLDMYK.APKEQRD..QLM..ERK.KAEVD.L.G...E.EE..RRESKK | |
| Retrocopy | HLKGLRAELKKAHESQKEMKLLLDMYKLAPKEQRDNQQLMEDERKVKAEVDQLQGHVQEMEEKYRRESKK |
| Parental | IADEDALRRIRQAEEQIEHLQRKLGATKQEEEALLSEMDVTGQAFEDMQEQNGRLLQQLREKDDANFKLM |
| .A.E.ALR...QA..QI..L.RKLGATK.EE.AL.SEM.VTGQAFE..QEQN.RL.QQL.EKD.ANFKL. | |
| Retrocopy | RAYERALRSNWQA-QQIKYLRRKLGATKREEDALASEMEVTGQAFEELQEQNQRLKQQLQEKDEANFKLL |
| Parental | SERIKANQIHKLLREEKDELGEQVLGLKSQVDAQLLTVQKLEEKERALQGSLGGVEKELTLRSQALELNK |
| SER...N.I.KLL.EEK.EL.EQVL.L.SQV.AQLLTVQ..E..E..LQG.LG.VE.EL.L..QALE..K | |
| Retrocopy | SERGETNDIYKLLCEEKSELEEQVLSLQSQVNAQLLTVQTMEHNEWILQGCLGSVERELMLCNQALEQTK |
| Parental | RK |
| .K | |
| Retrocopy | TK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Sorex araneus was not studied using RNA-Seq expression data.
Sorex araneus was not studied using ChIP-Seq data.
Sorex araneus was not studied using EST data.
Sorex araneus was not studied using FANTOM5 data.
retro_sara_299 was not experimentally validated.
Retrocopy orthology:
Sorex araneus 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000010964 | 1 retrocopy | |
| Sorex araneus | ENSSARG00000009524 | 1 retrocopy |
retro_sara_299 ,
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