RetrogeneDB ID: retro_itri_1585

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393558.1:433546..434448(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022859
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1585
CTGGCGCTCAACAAGAACCACTCGGAGGGTGGCAGAGTGATCGTCAACAACACTAAGCGTGTTCTAATATCCTATGATCA
TGTGGAACTTACATTTAATGACATGAAGAATGTTCCAGAGGCCTTCAAAGGGACAAAGAAGGGCACTGTCTACCTTACCC
CTTACTGGGTCATCTCTCTGTCCAAGGGGAAGGATGCCATGCAGTCCTTCATGATGCCATTTTATCTCATGAAGAACTAT
AAGATCAAACAGCCTGTGTTTGGTGCAAACTACATCAAGGGGATGGTAAAGGCTGAAGCAGGAGGTGGCTGGGAAGGCTC
TGCTTCATACAAGTTGACCTTCACAGCAGAGGGCGCCATCGAGCTTGGTCAGCGCATGCTACAGGTGGCATCTCAAGCTT
CCAGAGGTGAAGCCCCCAATGGAGCCTATGGATACCCTTCCATGCCCAGCGGGGCCTATTTCTTTCCCCTGCCAGTCGCC
AATGGAATGTATCCCTGCCCTCCTGGATACCCCTATCCACTGCCGCACCTGAGTTCTATCCAGGAGCTACTGTAATGGAT
GGGGCCATGGGATATGTGCAGCCCCCACCACCACCCTGTCCTGGACCCATGAAGCCTCCAGTCAGTGGCCCTAATGTCCC
CTCCACTCCTGCAGCTGAGGCCAAGGCCTCAGAAGCAGTTGCCAGTGCCTATTACAACCCAGGCAACCCACACAACGTCT
ACATGCCCACGAGCCAGCCTCCACCACCTCCCTACTACCCTCCAGAAGATAAGAAGACCCAGTAGACCCTGCCTACTTCC
CTGTCCCCACCTCATGGGCCTTCCGTACCCCTCCTTGTGGGACTGCATCTGACTGGGGGAGGCCAGGGAGGACCTTATTC
TTCCCCTGGTCTGATTATAAAA

Alignment

ORF - retro_itri_1585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 89.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALNKNHSEGGGVIVNNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSF
          .ALNKNHSEGG.VIVNNT...L.SYDHVELTFNDMKNVPEAFKGTKKGTVYLTPY.VI.LSKGKDAMQSF
Retrocopy LALNKNHSEGGRVIVNNTKRVLISYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYWVISLSKGKDAMQSF

Parental  MMPFYLMKDCEIKQPVFGANYIKGMVKAEAGGGWEGSASYKLTFTAGGAIEFGQRMLQVASQASRGEAPN
          MMPFYLMK...IKQPVFGANYIKGMVKAEAGGGWEGSASYKLTFTA.GAIE.GQRMLQVASQASRGEAPN
Retrocopy MMPFYLMKNYKIKQPVFGANYIKGMVKAEAGGGWEGSASYKLTFTAEGAIELGQRMLQVASQASRGEAPN

Parental  GAYGYPYMPSGAYVFPPPVANGMYPCPPGYPYPPP-PPEFYPGAPVMDGAMGYVQPPPPPYPGPMEPPVS
          GAYGYP.MPSGAY.FP.PVANGMYPCPPGYPYP.P..PEFYPGA.VMDGAMGYVQPPPPP.PGPM.PPVS
Retrocopy GAYGYPSMPSGAYFFPLPVANGMYPCPPGYPYPLP<APEFYPGATVMDGAMGYVQPPPPPCPGPMKPPVS

Parental  GPDVPSTPAAEAKAAEA-AASAYY-NPTHTTSTCPRASLHHLPTTLQKIRRPSR-PRLLP-SPPHGPSLP
          GP.VPSTPAAEAKA.EA.A...Y....THTTSTCPRASLHHLPTTLQKIRRPSR.P...P.SPPHGPS.P
Retrocopy GPNVPSTPAAEAKASEAVASAYYN>QATHTTSTCPRASLHHLPTTLQKIRRPSR>PAYFP>SPPHGPSVP

Parental  LLVGLHLAGGGQGGPYSSPGLMIK
          LLVGLHL.GGGQGGPYSSPGL.IK
Retrocopy LLVGLHLTGGGQGGPYSSPGLIIK

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_1585 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1585 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,