RetrogeneDB ID: retro_cjac_1285

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:57558220..57558800(-)
• Located in intron of: ENSCJAG00000010638

Retrocopy information

• Ensembl ID: ENSCJAG00000031711
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSRP2
• Ensembl ID: ENSCJAG00000019153
• Aliases: None
• Description: cysteine and glycine-rich protein 2 [Source:HGNC Symbol;Acc:2470]

Sequence

>retro_cjac_1285
ATGCCCGTCTGGGGCAGTGGAAACAAGTGTGGGGCCTGCGGGAGGGCCGTGTACCACACAGAAGAGGTGTCGTGTGATGG
CAAGAGCTTCCACTGCTGCTGCTTTCTCTGCATGGTTTGCAGGAAAAAATTAGACAGCACAACAGTGGCAACTTGCGATG
AAGAGATCTACTGTAAATCCTGCTACGGAAAGACGTATATGGGCCAAAAGGCTAGGGTTATGGCCAGGGCGCTGGCACGC
TTAACATGGACCATGGCGAGAGGCTGGGCATCAAACCAGAGAGTGTTCAGCCTCACAGGCCTACGACAAATCCAAACACT
TCTAAATTTGCTCAGAAATATGGAGGTGCTGAGAAGTGTTCCAGATGCGGGGATTCTGTATATGCTGCCGAGAAGATCAT
TGGAGCTGGAAAGCCCTGGCACAAAAACTGTTTCTGATGTGAAAAGTGTGGGAAGAGTCTTGAATTAACAACTCTGACTG
AAAAAGAAGGTGAAATCTATGGTAAAGGATGTTATGCAAAGAACTCTGGGCCCGGGGGATTTGGTATGGCCAAGGAGCAG
GGGCTCTTGTTCATGCTCAG

Alignment

ORF - retro_cjac_1285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKSCYGKKY-GPK
          MPVWG.GNKCGACGR.VYH.EEV.CDG.SFH.CCFLCMVCRK.LDSTTVA..DEEIYCKSCYGK.Y.G.K
Retrocopy MPVWGSGNKCGACGRAVYHTEEVSCDGKSFHCCCFLCMVCRKKLDSTTVATCDEEIYCKSCYGKTYMGQK

Parental  -GYGYGQGAGTLNMDRGERLGIKPESVQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIGAGKP
          .G.GYGQGAGTLNMD.GERLGIKPESVQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIGAGKP
Retrocopy <G*GYGQGAGTLNMDHGERLGIKPESVQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIGAGKP

Parental  WHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGFG-YGQGAGALVHAQ
          WHKNCF.C.KCGKSLE.TTLTEKEGEIY.KGCYAKN.GP.GFG.YGQGAGALVHAQ
Retrocopy WHKNCF*CEKCGKSLELTTLTEKEGEIYGKGCYAKNSGPGGFG<YGQGAGALVHAQ

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	0.04 RPM	2.24 RPM
SRP051959_heart	0.05 RPM	9.93 RPM
SRP051959_kidney	0.00 RPM	18.66 RPM
SRP051959_liver	0.00 RPM	2.34 RPM
SRP051959_lung	0.00 RPM	7.58 RPM
SRP051959_lymph_node	0.00 RPM	3.33 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.27 RPM
SRP051959_spleen	0.00 RPM	2.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1285 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1285 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019153	6 retrocopies	retro_cjac_1266, retro_cjac_1285 , retro_cjac_1384, retro_cjac_1555, retro_cjac_2919, retro_cjac_3150,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Equus caballus	ENSECAG00000015606	1 retrocopy	retro_ecab_412,
Echinops telfairi	ENSETEG00000019648	1 retrocopy	retro_etel_1589,
Homo sapiens	ENSG00000175183	2 retrocopies	retro_hsap_2833, retro_hsap_2836,
Gorilla gorilla	ENSGGOG00000026601	2 retrocopies	retro_ggor_1967, retro_ggor_1969,
Myotis lucifugus	ENSMLUG00000002384	3 retrocopies	retro_mluc_1888, retro_mluc_486, retro_mluc_720,
Macaca mulatta	ENSMMUG00000018257	1 retrocopy	retro_mmul_1474,
Mustela putorius furo	ENSMPUG00000017469	1 retrocopy	retro_mputfur_262,
Nomascus leucogenys	ENSNLEG00000004885	2 retrocopies	retro_nleu_1208, retro_nleu_1592,
Oryctolagus cuniculus	ENSOCUG00000008330	2 retrocopies	retro_ocun_1165, retro_ocun_649,
Otolemur garnettii	ENSOGAG00000013999	6 retrocopies	retro_ogar_1220, retro_ogar_1411, retro_ogar_1688, retro_ogar_2589, retro_ogar_2909, retro_ogar_3399,
Ochotona princeps	ENSOPRG00000011987	1 retrocopy	retro_opri_1125,
Pongo abelii	ENSPPYG00000004790	2 retrocopies	retro_pabe_2199, retro_pabe_2347,
Rattus norvegicus	ENSRNOG00000003772	1 retrocopy	retro_rnor_1763,
Sorex araneus	ENSSARG00000002290	1 retrocopy	retro_sara_526,
Ictidomys tridecemlineatus	ENSSTOG00000010876	1 retrocopy	retro_itri_551,
Tupaia belangeri	ENSTBEG00000009767	3 retrocopies	retro_tbel_1866, retro_tbel_4404, retro_tbel_4407,
Tursiops truncatus	ENSTTRG00000014596	1 retrocopy	retro_ttru_1332,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,