RetrogeneDB ID: retro_itri_480

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:2542587..2543032(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF5
• Ensembl ID: ENSSTOG00000024478
• Aliases: None
• Description: ring finger protein 5, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10068]

Sequence

>retro_itri_480
TGTTTGGAGACTGCTCAGGAAGCTGTGGTCAGTGTGTGTGGCCACCTGTACTGTTGGCCCTATCTTCCTCAGAGGCTGGA
AACACAGCCAGAGCAGCAAGAGTGCCCAATGTGCAAAGCTGTCATTGGCAGAGAGAAGGTTGTCCTGCTTTATGGACGAG
GGAGCCAGAAGCCCCAGGATCCCAGATTGGAAACTCCACCTCACCCCCAGGGCCAGCGACCTGCTCCAGAGAACAGTGGG
AGACTCCAGCCACTAGGTGATACCAGGGGTTTTCACTTCTCATTGGGTGTTGGTGCTTTTTCCTGTGATACCAACTGTCT
TCAATGCTTGTGAGCCTTTTCGCAGGGACGCAGGGGTGGGTCTGGGACAGGGTCACCCGGCCTCCAGCTGGCAGAATTCC
CTCTTCCTCTTTCTCGCCATCTTCTTTTTCTGGCTGCTCTGTATT

Alignment

ORF - retro_itri_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.97 %
• Parental protein coverage: 83.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAGISREKVVPLYGRGSQKPQDPRLKTPPRPQ
          CLETA.EAVVSVCGHLYCWP.L.Q.LET.PE.QECP.CKA.I.REKVV.LYGRGSQKPQDPRL.TPP.PQ
Retrocopy CLETAQEAVVSVCGHLYCWPYLPQRLETQPEQQECPMCKAVIGREKVVLLYGRGSQKPQDPRLETPPHPQ

Parental  GQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFT-TVFNAHEPFRRGAGVDLGQGHPASSWQDSLFLF
          GQRPAPE..G..QP.GDT.GFH..F..G...F...T.TVFNA.EPFRR.AGV.LGQGHPASSWQ.SLFLF
Retrocopy GQRPAPENSGRLQPLGDTRGFH--FSLGVGAFSCDT>TVFNACEPFRRDAGVGLGQGHPASSWQNSLFLF

Parental  LAIFFFFWLLSI
          LAI.FFFWLL.I
Retrocopy LAI-FFFWLLCI

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_480 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_480 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000016417	1 retrocopy	retro_ocun_1241,
Otolemur garnettii	ENSOGAG00000031466	1 retrocopy	retro_ogar_1951,
Oreochromis niloticus	ENSONIG00000013523	1 retrocopy	retro_onil_48,
Ochotona princeps	ENSOPRG00000004366	2 retrocopies	retro_opri_166, retro_opri_667,
Pan troglodytes	ENSPTRG00000018010	1 retrocopy	retro_ptro_2740,
Ictidomys tridecemlineatus	ENSSTOG00000024478	1 retrocopy	retro_itri_480 ,
Tupaia belangeri	ENSTBEG00000016320	1 retrocopy	retro_tbel_2183,