RetrogeneDB ID: | retro_itri_486 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393295.1:5702559..5703427(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SMARCD3 | ||
| Ensembl ID: | ENSSTOG00000009660 | ||
| Aliases: | None | ||
| Description: | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Source:HGNC Symbol;Acc:11108] |
Retrocopy-Parental alignment summary:
>retro_itri_486
GATGCCACAAAACAAAAGAGGAAATTTTCTTCCTTTTTTAAGTCCTTAGTGATCGAATTGGACAAAGACTTGTATGGGCC
AGACAACAATCTGGTAGAATGGCACAGGACTGCCACTACCCAGGAGACGGATGGCTTCCAGGTGAAGTGATCAGGAGATG
TGAATGGATGGTGTACTGTCCTACTGATGCTAGATTATCGGCCTCCCCAGTTTAAATTAGACTCTTGTTTGGCTCGGCTC
CTTGGCATTCACACCCAGACTCATCCAGTGATCATTCAAGCACTGTGGCAATACATAAAGACACATAAGCTCCAAGATCC
TCACAAGCGGGAGGTTTGTCATCTATGATAAGTACCTCCAGCAGATCTTTGAGTCTCAGCATATGAAGTTTTCAGAGATC
CCTCAAAGGCTGCATGCCTTGCTTATGCCACCAGAACCCATTATCATTAATCACGTCATCAGTATTGATCCAAATGATCA
GAAAAAGACAGCTTATTATGACGTTGATGTGGAAGTGGATGATACCTTAAAGACTCAGATGAATTCTTTCCTGCTGTCCA
CCGCCAGTCAACAGGAGATTGCTACTCTAGACAACAAGATTCACAAAACAATAGAAACTATCAACCAGCTCAAGACCTAG
TAGGAATTCATGCTGAGCTTTGCCAAATATCCTCAGGGTTTCATCAATGATTGGCTTCAGTCCCAGTGCTGGGACCTCAA
GACCATGACTGATGTGGTGGGTAACCCAGAGGAGGAGCAACGAGCTGAGTTCTATGTCCAGCCTTGGGCTCAGGAGGCCC
TGTGCCGATACTTTTACTCCAAGGTGCAGCAGAGACGACAAGAATTAGAGCAAGCCCTGGGAATCCGG
ORF - retro_itri_486 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.38 % |
| Parental protein coverage: | 59.47 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DPSKQKRKFSSFFKSLVIELDKDLYGPDNHLVEWHRTPTTQETDGFQVKRPGDLSVRCTLLLMLDYQPPQ |
| D..KQKRKFSSFFKSLVIELDKDLYGPDN.LVEWHRT.TTQETDGFQVK..GD....CT.LLMLDY.PPQ | |
| Retrocopy | DATKQKRKFSSFFKSLVIELDKDLYGPDNNLVEWHRTATTQETDGFQVK*SGDVNGWCTVLLMLDYRPPQ |
| Parental | FKLDPRLARLLGLHTQSRSAIVQALWQYVKTNRLQDSHDKE-YINGDKYFQQIFDCPRLKFSEIPQRLTA |
| FKLD..LARLLG.HTQ....I.QALWQY.KT..LQD.H..E.....DKY.QQIF.....KFSEIPQRL.A | |
| Retrocopy | FKLDSCLARLLGIHTQTHPVIIQALWQYIKTHKLQDPHKRE>FVIYDKYLQQIFESQHMKFSEIPQRLHA |
| Parental | LLLPPDPIVINHVISVDPSDQKKTACYDIDVEVEEPLKGQMSSFLLSTANQQEISALDSKIHETIESINQ |
| LL.PP.PI.INHVIS.DP.DQKKTA.YD.DVEV...LK.QM.SFLLSTA.QQEI..LD.KIH.TIE.INQ | |
| Retrocopy | LLMPPEPIIINHVISIDPNDQKKTAYYDVDVEVDDTLKTQMNSFLLSTASQQEIATLDNKIHKTIETINQ |
| Parental | LKIQRDFMLSFSRDPKGYVQDLLRSQSRDLKVMTDVAGNPEEERRAEFYHQPWSQEAVSRYFYCKIQQRR |
| LK....FMLSF...P.G...D.L.SQ..DLK.MTDV.GNPEEE.RAEFY.QPW.QEA..RYFY.K.QQRR | |
| Retrocopy | LKT**EFMLSFAKYPQGFINDWLQSQCWDLKTMTDVVGNPEEEQRAEFYVQPWAQEALCRYFYSKVQQRR |
| Parental | QELEQSLVVR |
| QELEQ.L..R | |
| Retrocopy | QELEQALGIR |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_486 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_486 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus 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 | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000009660 | 1 retrocopy |
retro_itri_486 ,
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