RetrogeneDB ID: retro_itri_1885

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394688.1:4384..4994(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026097
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB6C
• Ensembl ID: ENSSTOG00000023497
• Aliases: None
• Description: RAB6C, member RAS oncogene family [Source:HGNC Symbol;Acc:16525]

Sequence

>retro_itri_1885
TCCGTGGGTGGAGACTTCAGGAATCCTCTGAGGAAATTCAAGCTAGGAAAACAGAGCATTGGAAAAACATCCTTGATCAC
CAGATTCATGTATGACAGTGTTGACAACACTTATCAGGCAACAATTCGCATTGACTTTTTATCAAAAACCATGTCCTTGG
AGGATCGAACAGTACGATTGCAATTATGGGACACAGAGGTCAAGAGCGGTTCAGGAGCTTGATTCCTAGCTACATTCGTG
ACTCCACTATGGCAGTCATTTTTTATGATATCACAAATGTTAACGCATTCCAGCAAACTACAAAATGGATTGATGATGTC
AGAACAGAAAGTGGAAGTGATGTTATCATCATGCTAGTAGGAAATAAAACAGATCTTGCTGACAAGAGGCAAGTTTCAAT
TGAGGAAGGAGAGAGGAAAGCCAAAGAGCTGAATTTTAATTTCATTGAAACCAGAGCAAAAGCAGGATACAATAAAGCAG
CTCTTCCGACGTGTAGCAGCAGGCTTTGCCTGGAATGGAAAGCACACAAGACAGAAGCAGAGAAGACATGATTGACATTA
AAGTGGAAAAGCCTCAGGAGCAACCAGTCAGTGAAGGAGGCTGTTCCTGC

Alignment

ORF - retro_itri_1885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAGGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTIRLQLWDTA-
          S.GGDF.NPLRKFK...LG.QS.GKTSLITRFMYDS.DNTYQATI.IDFLSKTM.LEDRT.RLQLWDT..
Retrocopy SVGGDFRNPLRKFK---LGKQSIGKTSLITRFMYDSVDNTYQATIRIDFLSKTMSLEDRTVRLQLWDTE<

Parental  GQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGN-KTDLADKRQVSIE
          GQERFRSLIPSYIRDS..AV..YDITNVN.FQQTTKWIDDVRTE.GSDVIIMLVGN.K..L.........
Retrocopy GQERFRSLIPSYIRDSTMAVIFYDITNVNAFQQTTKWIDDVRTESGSDVIIMLVGN>KQILLTRGKFQLR

Parental  EGERKAKELNVMFIETSAKAGYNVKQLFRRVAA-ALPGMESTQDRSREDMIDIKLEKPQEQPVSEGGCSC
          ....K.K...........K.....KQLFRRVAA.ALPGMESTQDRSREDMIDIK.EKPQEQPVSEGGCSC
Retrocopy KERGKPKS*ILISLKPEQKQD-TIKQLFRRVAA>ALPGMESTQDRSREDMIDIKVEKPQEQPVSEGGCSC

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_1885 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1885 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000992	1 retrocopy	retro_chof_859,
Homo sapiens	ENSG00000175582	1 retrocopy	retro_hsap_7,
Mus musculus	ENSMUSG00000030704	1 retrocopy	retro_mmus_2400,
Nomascus leucogenys	ENSNLEG00000017098	1 retrocopy	retro_nleu_200,
Ochotona princeps	ENSOPRG00000010355	6 retrocopies	retro_opri_1082, retro_opri_1085, retro_opri_1095, retro_opri_1118, retro_opri_247, retro_opri_858,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,
Ictidomys tridecemlineatus	ENSSTOG00000023497	3 retrocopies	retro_itri_1743, retro_itri_1827, retro_itri_1885 ,