RetrogeneDB ID: retro_cjac_440

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82907582..82908253(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004022
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STOML2
• Ensembl ID: ENSCJAG00000009137
• Aliases: None
• Description: stomatin (EPB72)-like 2 [Source:HGNC Symbol;Acc:14559]

Sequence

>retro_cjac_440
CAGACAGAGCTCAGCAAACTCTCTCTGGACAAAGTCTTCCGGGAACGGGAGTCCCTGAATGCGAGCATTGTGGATGCCAT
CAACCAGGCTGCTGACTGCTGGGGTATCCAGCTGCCTTCGTTACGAGATCAGGGATATCCATGTGCCATCCCAGGTGAAA
GTCTATGCAGATGCAGGTGGAGGCAGAACGGCGGAAAGGGGCCACAGTTCTAGAGTCTGAGGGGCCCCGAGAGTCGGCCA
TCAACATGGCAGAGGGGAAGAAACAGGCCCAGATCCTGGCCTCTGAAGCAGAAAAGCCTGAACAGATAAATCAAGCAGCA
GGAGAAGCCAGTGCAGTTCCCGCCAAGGCCAAGGCGAGGGCTAAAGCTGAAGCTATTCGAATCCTGGCTGCAGCTCTGAC
ACAACATAATGGAGATGCAGCAGCTTCACTGACTGTGGCGGAGCAGTATGTCAGCGCATTCTCCAAACTCGCCAAGGACT
CCAACACTATCCTGCTGCCCTCCAATCCTGGTGATGTCCCCAGCATGGTGGCTCAGGCCATGGGTGTATATGGAGCCCTC
ACCAAAGCCCCAGCACCAGGGGCTCCACACTCGGTCTCCAGCGGGAGTAGCAGAGATGTCCAGAGTACAGATGCGAGTCT
TGATGAGGAACTTGAAGGAATCAAGTTGAGT

Alignment

ORF - retro_cjac_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 62.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSELGKLSLDKVFRERESLNASIVDAINQAADCWGIR-CLRYEIKDIHVP-PRVKESMQMQVEAERRKRA
          ..EL.KLSLDKVFRERESLNASIVDAINQAADCWGI..CLRYEI.DIHVP.PR.K.SMQMQVEAERRK.A
Retrocopy QTELSKLSLDKVFRERESLNASIVDAINQAADCWGIQ>CLRYEIRDIHVP>PR*K-SMQMQVEAERRKGA

Parental  TVLESEGTRESAINVAEGKKQAQILASEAEKAEQINQAAGEASAVLAKAK--AKAEAIRILAAALTQHNG
          TVLESEG.RESAIN.AEGKKQAQILASEAEK.EQINQAAGEASAV.AKAK..AKAEAIRILAAALTQHNG
Retrocopy TVLESEGPRESAINMAEGKKQAQILASEAEKPEQINQAAGEASAVPAKAKARAKAEAIRILAAALTQHNG

Parental  DAAASLTVAEQYVSAFSKLAKDSNTILLPSNPGDVTSMVAQAMGVYGALTKAPAPGDPHSVSSGSSRDVQ
          DAAASLTVAEQYVSAFSKLAKDSNTILLPSNPGDV.SMVAQAMGVYGALTKAPAPG.PHSVSSGSSRDVQ
Retrocopy DAAASLTVAEQYVSAFSKLAKDSNTILLPSNPGDVPSMVAQAMGVYGALTKAPAPGAPHSVSSGSSRDVQ

Parental  STDASLDEELDRVKLS
          STDASLDEEL...KLS
Retrocopy STDASLDEELEGIKLS

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	10.85 RPM
SRP051959_heart	0.00 RPM	9.73 RPM
SRP051959_kidney	0.00 RPM	12.22 RPM
SRP051959_liver	0.00 RPM	19.10 RPM
SRP051959_lung	0.02 RPM	9.65 RPM
SRP051959_lymph_node	0.00 RPM	9.13 RPM
SRP051959_skeletal_muscle	0.00 RPM	19.37 RPM
SRP051959_spleen	0.02 RPM	10.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_440 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000000485	1 retrocopy	retro_cint_6,
Callithrix jacchus	ENSCJAG00000009137	1 retrocopy	retro_cjac_440 ,
Ciona savignyi	ENSCSAVG00000000950	1 retrocopy	retro_csav_5,
Microcebus murinus	ENSMICG00000005517	1 retrocopy	retro_mmur_571,
Mus musculus	ENSMUSG00000028455	1 retrocopy	retro_mmus_1034,
Oryctolagus cuniculus	ENSOCUG00000006451	1 retrocopy	retro_ocun_695,