RetrogeneDB ID: retro_itri_1188

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393396.1:2475071..2475785(+)
• Located in intron of: ENSSTOG00000011936

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSSTOG00000027197
• Aliases: None
• Description: RNA binding motif protein 22 [Source:HGNC Symbol;Acc:25503]

Sequence

>retro_itri_1188
TACAGACATGAGAAGCCTACAGATCCAGATGACCCCCTTGCTGATCAAAATATTAAAGACCGTTATTATGGAATCAGTGA
CCCTGTAGCAGATAAGCTTCTAACGCAGGCTTCAATAATGCCTCGTCTGGACCCACCGGAGGATAAAACTATCACCACAC
TAGATGTTGGTGGTCCGGGTGATACCATTACTGAGACAGATCTCATAAATCATTTCTACCAGTTTGGAGAGATTCGAAGG
ATCACTGTAGTACAGAGACAGCAGTGTGCGCTCATCCAGTTTGCCACAAGGCAGGCTGCAGAAGTGGCTGCTGAGAAGTC
CTTTAATAAGTTGATTGTCAGTGGATGCAGACTCAAGGTGAAATGGGGACGATCCCCAGCAGCCAGAGGAGAAGAAAAAG
AGAAGGATGGAACCAAAGATTCTGGGACCCAGCTGGAGCCTGTTCCAGGACTGCCTGGAGCTCTTCCTCCTCCTCCTGCA
GCAGAAGAAGCCTCTGCCAGCTACTTCAACCTCCTCCCGAGTGGCCCTCCAGCCGTGGTAAACACTGCCCTGCCACCACT
GCCTGGGACTGCCCCATCCCCACCCCCAGGTTTGGGGCCACACATGGTCCACCCAATGAGACCACCTGCTCCTTTCATGA
GGGCTCCAGGACCAATCCACTCTCCTTCTCAGGACCCTCAGAGGATGGGAGCACATGCTGGAAGATACAGCAGT

Alignment

ORF - retro_itri_1188 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 58.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRN
          .RHEKPTDPDDPLADQNIKDRYYGI.DPVADKLL..AS.MPRLDPPEDKTITTL.VGG.GDTITETDL.N
Retrocopy YRHEKPTDPDDPLADQNIKDRYYGISDPVADKLLTQASIMPRLDPPEDKTITTLDVGGPGDTITETDLIN

Parental  HFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTD
          HFYQFGEIR.ITVVQRQQCA.IQFATRQAAEVAAEKSFNKLIV.G.RL.VKWGRS.AARG.EKEKDGT.D
Retrocopy HFYQFGEIRRITVVQRQQCALIQFATRQAAEVAAEKSFNKLIVSGCRLKVKWGRSPAARGEEKEKDGTKD

Parental  SGIKLEPVPGLPGALPPPPAAEEEASANYFNLPPSGPPAVVNIALPPPPGIAPPPPPGFGPHMFHPMGPP
          SG..LEPVPGLPGALPPPPAA.EEASA.YFNL.PSGPPAVVN.ALPP.PG.AP.PPPG.GPHM.HPM.PP
Retrocopy SGTQLEPVPGLPGALPPPPAA-EEASASYFNLLPSGPPAVVNTALPPLPGTAPSPPPGLGPHMVHPMRPP

Parental  PPFMRAPGPIHYPSQDPQRMGAHAGKHSS
          .PFMRAPGPIH.PSQDPQRMGAHAG..SS
Retrocopy APFMRAPGPIHSPSQDPQRMGAHAGRYSS

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_1188 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1188 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Nomascus leucogenys	ENSNLEG00000010397	2 retrocopies	retro_nleu_1691, retro_nleu_1800,
Ictidomys tridecemlineatus	ENSSTOG00000027197	1 retrocopy	retro_itri_1188 ,