RetrogeneDB ID: retro_cjac_1814

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:73023279..73023981(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013010
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011407
• Aliases: None
• Description: None

Sequence

>retro_cjac_1814
GGCGGACAGGGACCCGTAGCGCCCAAAGCCAGAGTACACTTCCGAGTGGCGAGGTTCATCATGGAGCCAGGTGTCAAGCT
GGGGATGTGGTCCCTTCCCATTGCCACTGCTTGCACCATTTACCATAAGTTCTTCTGTCAGACCAACCTGGATGCCTATG
ACCCTTACTTGATCGCTATGTCTTCCATTTACTTGGCTGGCAAAGTGGAAGAGCAGCATCTGTGGACTCGTGATATCATC
GATGTGTCCAACAGGTACTTTAACCCAAATGGTGAGCCCCTGGAGTTGGACTCCCGCTTCTGGGAGCTCCGAGACAGCAT
TGTGCAGTGCGAGCTTCTCATGCTGAGAGTTCTGCGCTTCCAGGTCTCCTTCCAGCACCCACACAAGTACCTGCTCCACT
ACCTGGTTTCCCTCAAGAACTGGATGAACCTCCACAGCTGGCAGCGGACTCCTGTTGCCGTCACTGCCTGGGCCCTGCTG
CGGGACAGCTACCACGGGGGGCTGTGCCTCTGCTTCCAGGCCCAGCACATAGCCGTGGCAGTGCTCTACCTGGCCCTGCA
GCTTTATGGAGTCAAGGTACCTGCTGAGGTTGAGGCTGAGAAGCCATGGTGGCAGGTATTTAGTGATGACCTTACCAAGC
CAATCATTGATAATATTGTGTCTGATCTCATTCAGATTTATTCCATGGACACAGAGATCCCC

Alignment

ORF - retro_cjac_1814 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 94.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPEGRPAPEARVHFRVARFIMEAGVKLGMRSIPIATACTIYHKFFCESSLDAYDPYLVAMSSIYLAGKVE
          G..G..AP.ARVHFRVARFIME.GVKLGM.S.PIATACTIYHKFFC...LDAYDPYL.AMSSIYLAGKVE
Retrocopy GGQGPVAPKARVHFRVARFIMEPGVKLGMWSLPIATACTIYHKFFCQTNLDAYDPYLIAMSSIYLAGKVE

Parental  EQHLRTRDIINVSNRYLDPSGEPLELDSRFWELRDSIVQCELLVLRVLRFQVSFQHPHKYLLHYLVSFKN
          EQHL.TRDII.VSNRY..P.GEPLELDSRFWELRDSIVQCELL.LRVLRFQVSFQHPHKYLLHYLVS.KN
Retrocopy EQHLWTRDIIDVSNRYFNPNGEPLELDSRFWELRDSIVQCELLMLRVLRFQVSFQHPHKYLLHYLVSLKN

Parental  WLNRHSWQRTPVAVTAWALLRDSYHGGLCLRFQAQHIAVAVLYLALQVYGVEVPAEVEAEKPWWQVFSDD
          W.N.HSWQRTPVAVTAWALLRDSYHGGLCL.FQAQHIAVAVLYLALQ.YGV.VPAEVEAEKPWWQVFSDD
Retrocopy WMNLHSWQRTPVAVTAWALLRDSYHGGLCLCFQAQHIAVAVLYLALQLYGVKVPAEVEAEKPWWQVFSDD

Parental  LTKPIIDNIVSDLIQIYAMDTEIP
          LTKPIIDNIVSDLIQIY.MDTEIP
Retrocopy LTKPIIDNIVSDLIQIYSMDTEIP

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	1.97 RPM	2.40 RPM
SRP051959_heart	0.82 RPM	2.39 RPM
SRP051959_kidney	0.62 RPM	2.46 RPM
SRP051959_liver	0.54 RPM	2.47 RPM
SRP051959_lung	2.31 RPM	2.75 RPM
SRP051959_lymph_node	2.58 RPM	2.97 RPM
SRP051959_skeletal_muscle	0.68 RPM	1.48 RPM
SRP051959_spleen	1.74 RPM	2.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1814 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1814 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780,
Callithrix jacchus	ENSCJAG00000006738	1 retrocopy	retro_cjac_1273,
Callithrix jacchus	ENSCJAG00000011407	1 retrocopy	retro_cjac_1814 ,
Dipodomys ordii	ENSDORG00000012846	1 retrocopy	retro_dord_420,
Gorilla gorilla	ENSGGOG00000027073	2 retrocopies	retro_ggor_2302, retro_ggor_911,
Macaca mulatta	ENSMMUG00000011480	1 retrocopy	retro_mmul_557,
Nomascus leucogenys	ENSNLEG00000013298	2 retrocopies	retro_nleu_1493, retro_nleu_2416,
Otolemur garnettii	ENSOGAG00000033279	1 retrocopy	retro_ogar_70,