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 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]

Sequence

>retro_itri_486
GATGCCACAAAACAAAAGAGGAAATTTTCTTCCTTTTTTAAGTCCTTAGTGATCGAATTGGACAAAGACTTGTATGGGCC
AGACAACAATCTGGTAGAATGGCACAGGACTGCCACTACCCAGGAGACGGATGGCTTCCAGGTGAAGTGATCAGGAGATG
TGAATGGATGGTGTACTGTCCTACTGATGCTAGATTATCGGCCTCCCCAGTTTAAATTAGACTCTTGTTTGGCTCGGCTC
CTTGGCATTCACACCCAGACTCATCCAGTGATCATTCAAGCACTGTGGCAATACATAAAGACACATAAGCTCCAAGATCC
TCACAAGCGGGAGGTTTGTCATCTATGATAAGTACCTCCAGCAGATCTTTGAGTCTCAGCATATGAAGTTTTCAGAGATC
CCTCAAAGGCTGCATGCCTTGCTTATGCCACCAGAACCCATTATCATTAATCACGTCATCAGTATTGATCCAAATGATCA
GAAAAAGACAGCTTATTATGACGTTGATGTGGAAGTGGATGATACCTTAAAGACTCAGATGAATTCTTTCCTGCTGTCCA
CCGCCAGTCAACAGGAGATTGCTACTCTAGACAACAAGATTCACAAAACAATAGAAACTATCAACCAGCTCAAGACCTAG
TAGGAATTCATGCTGAGCTTTGCCAAATATCCTCAGGGTTTCATCAATGATTGGCTTCAGTCCCAGTGCTGGGACCTCAA
GACCATGACTGATGTGGTGGGTAACCCAGAGGAGGAGCAACGAGCTGAGTTCTATGTCCAGCCTTGGGCTCAGGAGGCCC
TGTGCCGATACTTTTACTCCAAGGTGCAGCAGAGACGACAAGAATTAGAGCAAGCCCTGGGAATCCGG

Alignment

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_486 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_486 was not experimentally validated.

Homology

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.

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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 ,