RetrogeneDB ID: retro_cjac_3894

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286112.1:27614..28097(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7B
• Ensembl ID: ENSCJAG00000013630
• Aliases: None
• Description: COP9 signalosome subunit 7B [Source:HGNC Symbol;Acc:16760]

Sequence

>retro_cjac_3894
AGCTTGGCATCAAGAATGAAGTGTATTGCCTACTCTGTGTTGCTGAAAGACCTGGAGATGCAGAATCTTTGGGAACTAGA
AGACCTCATCATTGTGACTGTCTACACTGACATCATCCAGGGCAGCCTGGACCAGCAAAACCAGCTGCTGGAAGTGGATT
TCTGCATTGGCTGTGATATCCGAAAGAATGATATCAATAATATTGTCAAGACCCTGCATGAATTGTGTGACGACTGTGAA
GCAGTTCTGCTGGGCATCGAGCAGCAAGTTCTGAGTGTCAACTAGTACAAAGAAAACCACAACCGAACTCAGCAGCTGGT
AGAAGCAGAGGTAACCAACATCAAGAAGACACTCAAAGCCACCACATCCTCTTCGGCTCAGGAAATGGAGCAGCAGCTGG
CTGAACAGGAGTGTCCTTCTCACGCTGAGCAGAGGCAGCCCACCAAGATGTCTAAAGTGAAAGGTCTGGTCTCCAGCCGC
CAC

Alignment

ORF - retro_cjac_3894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.27 %
• Parental protein coverage: 61.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLASRMKCIPYSVLLKDLEMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVK
          SLASRMKCI.YSVLLKDLEM.NL.ELEDLII..VYTDIIQG.LDQ.NQLLEVDFCIG.DIRK.DINNIVK
Retrocopy SLASRMKCIAYSVLLKDLEMQNLWELEDLIIVTVYTDIIQGSLDQQNQLLEVDFCIGCDIRKNDINNIVK

Parental  TLHEWCDGCEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAERECPP
          TLHE.CD.CEAVLLGIEQQVL..N.YKENHNRTQQ.VEAEVTNIKKTLKAT.SSSAQEMEQQLAE.ECP.
Retrocopy TLHELCDDCEAVLLGIEQQVLSVN*YKENHNRTQQLVEAEVTNIKKTLKATTSSSAQEMEQQLAEQECPS

Parental  HAEQRQPTKKMSKVKGLVSSRH
          HAEQRQPT.KMSKVKGLVSSRH
Retrocopy HAEQRQPT-KMSKVKGLVSSRH

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	0.27 RPM	2.95 RPM
SRP051959_heart	0.42 RPM	4.72 RPM
SRP051959_kidney	0.13 RPM	4.84 RPM
SRP051959_liver	0.15 RPM	4.40 RPM
SRP051959_lung	0.59 RPM	5.86 RPM
SRP051959_lymph_node	0.94 RPM	4.93 RPM
SRP051959_skeletal_muscle	0.13 RPM	3.49 RPM
SRP051959_spleen	0.50 RPM	5.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3894 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3894 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013630	1 retrocopy	retro_cjac_3894 ,
Oryctolagus cuniculus	ENSOCUG00000016918	1 retrocopy	retro_ocun_1194,
Ochotona princeps	ENSOPRG00000008376	1 retrocopy	retro_opri_850,
Sarcophilus harrisii	ENSSHAG00000009961	1 retrocopy	retro_shar_537,