RetrogeneDB ID: retro_cfam_1038

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:40889382..40889993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP2
• Ensembl ID: ENSCAFG00000004946
• Aliases: None
• Description: WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]

Sequence

>retro_cfam_1038
TCAACAATATTGATCCTAATGTCCTATGACTATACAGAGTTTGTGTTCAAGGATGTGAAGAACATACCAGAGGCCTTCAA
AGGGACCAAGAAAGGCAACGTCTACTTTACCCCTTACCAGTTCCATTTTTCTGTCCAAAGGAAAGATGCCATCCAATCCT
TCATGATGCCATTTATCTGATAAAGGACTGCAAAATCAAGCAGCCTGTATTTGGTATAAATTACAGCAAAGAATAGTGAA
GGCTGAGAAGCAGGAAGTGGCTGGAAAGACTTCTTTATATGAGACGACCTTTACACCAAGAGGCACCATTGAGTTGCACA
ATAGATGATACAGGTAACATCTCAATCCTCCAAAGGTGAAGCCTCCAATGGACCCTGCAGGTACTCTCATATGCCCAGGA
GGGCTTTTGTCTTTCCCCTGCCAAGTACCAATGGAATGCATGCATGCCCATCTGTATGGGTACTTCCATCCACCGCTCCA
TCTGACTTCTACCCAGGACCTCCCATGATGAACTGAACATGGAATAGTTGGAACCATGGCCACCACCCTATTCTGGGCTC
CCGAAACCTCCAGCCACCAGCCCCGACATTCCCTCCACTCCTGCAGCTGAA

Alignment

ORF - retro_cfam_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.82 %
• Parental protein coverage: 77.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRV-IFLSKG-KDAMQSFMMPF-YLMKDCEIK
          .T..ILMSYD..E..F.D.KN.PEAFKGTKKG.VY.TPY...IFLSKG.KDA.QSFMMPF.YL.KDC.IK
Retrocopy STILILMSYDYTEFVFKDVKNIPEAFKGTKKGNVYFTPYQF>IFLSKG<KDAIQSFMMPF<YLIKDCKIK

Parental  QPVFGANYIK-GTVKAEAGGGWEGAASYKLTFTAGGAIEFGQR-MLQVASQASRGEAPNGAYGYSYTPSG
          QPVFG.NY.K...VKAE..........Y..TFT..G.IE...R.M.QV.SQ.S.GEA.NG...YS..P..
Retrocopy QPVFGINYSK<RIVKAEKQEVAGKTSLYETTFTPRGTIELHNR<MIQVTSQSSKGEASNGPCRYSHMPRR

Parental  AYVFPPPVANGMYPCPPGYPYPPPPPAEFYPGPPMMDGA-MGYVQPPPPPYPGPMEPPVSGPDVPSTPAA
          A.VFP.P..NGM..CP.....P...P..FYPGPPMM....M....P.PPPY.G...PP...PD.PSTPAA
Retrocopy AFVFPLPSTNGMHACPSVWVLPSTAPSDFYPGPPMMN*T<ME*LEPWPPPYSGLPKPPATSPDIPSTPAA

Parental  E
          E
Retrocopy E

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.13 RPM	131.25 RPM
SRP017611_brain	0.00 RPM	138.78 RPM
SRP017611_kidney	0.07 RPM	87.57 RPM
SRP017611_liver	0.00 RPM	37.56 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1038 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1038 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004946	1 retrocopy	retro_cfam_1038 ,
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
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,