RetrogeneDB ID: retro_cjac_575

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82898097..82898541(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WBP2
• Ensembl ID: ENSCJAG00000037619
• Aliases: None
• Description: WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]

Sequence

>retro_cjac_575
ATGGCGCTCAACAAGAATCACTCGAAGGGCAGTGGAGTGATCGTCAACAACACCGAAAGCATCCTAATGTCCTATGATCA
TGTGGAACTCACATTCAATGACATGAAGAACGTGCCAGAAGCCTTCAAAGGGACCAAGAAAGGCACCGTCTACCTTACCC
CTTACCAGGTCATCTTTCTGTCCAAGGGGCAGGATGCCATGCAGTCCTTCATGATGCCATTCTATCTCATGAAAGACTCT
GAGATCAAGCAGCCTGTGTTTGGTGCAAACTACATCAACGGAACAGTGAAGGCCGAAGCGGGAGGTGGCTGGGGAGGCTC
TGCTTCCTGCAAGCTGACGTTCATGGCAGGGGGCGCCATAGAGTTCGGACAGCGGATGCTCCAGGTGGCATCTCAAGCCT
CCAGAGGTGAAGCCCCCAATGGAGCCTATGGCTACTCTTACTTA

Alignment

ORF - retro_cjac_575 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.92 %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALNKNHSEGGGVIVNNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSF
          MALNKNHS.G.GVIVNNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPY.VIFLSKG.DAMQSF
Retrocopy MALNKNHSKGSGVIVNNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYQVIFLSKGQDAMQSF

Parental  MMPFYLMKDCEIKQPVFGANYIKGTVKAEAGGGWEGSASYKLTFMAGGAIEFGQRMLQVASQASRGEAPN
          MMPFYLMKD.EIKQPVFGANYI.GTVKAEAGGGW.GSAS.KLTFMAGGAIEFGQRMLQVASQASRGEAPN
Retrocopy MMPFYLMKDSEIKQPVFGANYINGTVKAEAGGGWGGSASCKLTFMAGGAIEFGQRMLQVASQASRGEAPN

Parental  GAYGYSYM
          GAYGYSY.
Retrocopy GAYGYSYL

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
SRP051959_colon	0.00 RPM	6.28 RPM
SRP051959_heart	0.00 RPM	13.40 RPM
SRP051959_kidney	0.00 RPM	17.82 RPM
SRP051959_liver	0.00 RPM	9.21 RPM
SRP051959_lung	0.02 RPM	11.79 RPM
SRP051959_lymph_node	0.02 RPM	7.88 RPM
SRP051959_skeletal_muscle	0.02 RPM	12.71 RPM
SRP051959_spleen	0.00 RPM	8.57 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_575 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_575 has 0 orthologous retrocopies within eutheria group .

---

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,