RetrogeneDB ID: retro_cjac_2396

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:161196842..161197217(+)
• Located in intron of: ENSCJAG00000011908

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSCJAG00000020761
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_cjac_2396
CGGAATGATTTTCAGAGGATTCCAGAACTTGCTGTCAACCCAGTGGGGGACTGGGTCATCAGTGCCTTCTTTCCAGAGGG
AGAGGACCAGATAAACTCTGTGGATTCCTGCGAACTTTGGCTTATATCCGAACCATTGAGGATAATGAAGAGAGCAAAGA
TGTGAATGGACCTGAACCACTCAGCAACAAATAGCACTTTGCTTCTGGACTATATTAGTTGGATAAAGATGACAAGACCT
CCTGTGATGAGCTGTTAGCAGGCGCCATGCGTGATGGTCCAAGTTAATGTCTCAGATGAGCAGCTGAGCGGCGGCGCAGA
CAGGACCATTCGGGAGGCTGATCCGCGTGGGGACAGTGACATATCTTTATCACAG

Alignment

ORF - retro_cjac_2396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.46 %
• Parental protein coverage: 65.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REDFQRIPELAINPLGDRIINAFFPEGEDQVN-FRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLH
          R.DFQRIPELA.NP.GD..I.AFFPEGEDQ.N...GF.RTLA..R.IEDNE.SKDVNGPEPL...SNK.H
Retrocopy RNDFQRIPELAVNPVGDWVISAFFPEGEDQIN<LCGFLRTLAYIRTIEDNEESKDVNGPEPL---SNK*H

Parental  FAFRLYDLDKDDKISRDELL-QVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTE
          FA..LY.LDKDDK.S.DELL.Q....MV.VN.SDEQL...ADRTI.EAD..GDS.IS...
Retrocopy FASGLY*LDKDDKTSCDELL>QAPCVMVQVNVSDEQLSGGADRTIREADPRGDSDISLSQ

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	0.22 RPM	23.23 RPM
SRP051959_heart	0.46 RPM	7.93 RPM
SRP051959_kidney	0.58 RPM	31.75 RPM
SRP051959_liver	0.09 RPM	85.19 RPM
SRP051959_lung	0.42 RPM	13.70 RPM
SRP051959_lymph_node	0.57 RPM	6.03 RPM
SRP051959_skeletal_muscle	0.26 RPM	7.64 RPM
SRP051959_spleen	0.36 RPM	7.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2396 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396 ,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207,