RetrogeneDB ID: retro_itri_660

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:741710..742355(-)
• Located in intron of: ENSSTOG00000008074

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP2
• Ensembl ID: ENSSTOG00000021421
• Aliases: None
• Description: WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]

Sequence

>retro_itri_660
TCAAACACTGAGAGCATCCTAATGTCCTATGAGCATGTGAAACTTAAACTCAATGACATGAAGAATATGTCAGAGATCTT
CAAAGAGAACAAGAAAGGCACTGTCTACCTTACCCCTTACAGGGTCAACTTTCTGTCCAAGGGGAAGGAGGCCATGCAGT
CCTTCATGATACCATTTTATCTCATGAAGGACTGTGAGATCAAGTAGCCTGTGTTGGTGCAAACTGCCAAGGGAACAGCA
AAGGCTAAAATTGGAGGTGGCTGGGAAGGCTCTGCTACAGATAATTTGACCTTCACAACAGGGGGCACCATCAAGTTTAG
TCAATGGATTCTCCAGATGGCATTTCAAGCCCCAGAAGTGAAGCCCTCAATGGAGCCTATGGGTACCCTTAATGCCTAGT
GGGGCCTGTTTTTCCCCCACCAGTTGCCAATGGAATATACCACTGCCTTCCTACCTAACCCATACACTGCCCCCATCTCA
TTTCTATTCAGGACACCCTCTGAAGGATGGGGCCATGGGATATGTGAAGCTTCCGCTTCCACCTTATCCTAGACCCATGA
AACCACAGTCAGCAGCCCTGATGTCCCCTCCACTACTGCGGCCATGGCCAAGCCCATAGAAGTAGCTACCAGTGCCTATT
ATAAC

Alignment

ORF - retro_itri_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.96 %
• Parental protein coverage: 65.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSFMMPFYLMKDCEIKQP
          .NTESILMSY.HV.L..NDMKN..E.FK..KKGTVYLTPYRV.FLSKGK.AMQSFM.PFYLMKDCEIK.P
Retrocopy SNTESILMSYEHVKLKLNDMKNMSEIFKENKKGTVYLTPYRVNFLSKGKEAMQSFMIPFYLMKDCEIK*P

Parental  VFGANYIKGMVKAEAGGGWEGSASYKLTFTAGGAIEFGQRMLQVASQA-SRGEAPNGAYGY-PYMPSGA-
          V......KG..KA..GGGWEGSA...LTFT.GG.I.F.Q..LQ.A.QA..R.EA.NGAYGY.P.MPSGA.
Retrocopy VL-VQTAKGTAKAKIGGGWEGSATDNLTFTTGGTIKFSQWILQMAFQA<PRSEALNGAYGY<PLMPSGA<

Parental  YVFP-PPVANGMYPCPPGYP-YPPPPPEFYPGAPVMDGAMGYVQPPPPPYPGPMEP-PVSGPDVPSTPAA
          ..FP.PPVANG.Y.C.P..P....PP..FY.G.P..DGAMGYV..P.PPYP.PM.P..VS.PDVPST.AA
Retrocopy LFFP<PPVANGIYHCLPT*P<HTLPPSHFYSGHPLKDGAMGYVKLPLPPYPRPMKP<TVSSPDVPSTTAA

Parental  EAKAAEAAASAYYN
          .AK..E.A.SAYYN
Retrocopy MAKPIEVATSAYYN

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_660 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_660 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004946	1 retrocopy	retro_cfam_1038,
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
Felis catus	ENSFCAG00000005760	1 retrocopy	retro_fcat_1454,
Homo sapiens	ENSG00000132471	1 retrocopy	retro_hsap_1926,
Gorilla gorilla	ENSGGOG00000009241	2 retrocopies	retro_ggor_1404, retro_ggor_698,
Macropus eugenii	ENSMEUG00000000070	1 retrocopy	retro_meug_579,
Macaca mulatta	ENSMMUG00000009381	2 retrocopies	retro_mmul_1062, retro_mmul_854,
Monodelphis domestica	ENSMODG00000007725	3 retrocopies	retro_mdom_1410, retro_mdom_1847, retro_mdom_375,
Mustela putorius furo	ENSMPUG00000013775	1 retrocopy	retro_mputfur_645,
Nomascus leucogenys	ENSNLEG00000001625	1 retrocopy	retro_nleu_1214,
Ochotona princeps	ENSOPRG00000006045	2 retrocopies	retro_opri_301, retro_opri_851,
Pongo abelii	ENSPPYG00000008640	3 retrocopies	retro_pabe_693, retro_pabe_75, retro_pabe_913,
Pan troglodytes	ENSPTRG00000009660	1 retrocopy	retro_ptro_15,
Ictidomys tridecemlineatus	ENSSTOG00000021421	2 retrocopies	retro_itri_1585, retro_itri_660 ,