RetrogeneDB ID: retro_cjac_2350

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:84801218..84801970(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006356
• Aliases: None
• Description: None

Sequence

>retro_cjac_2350
ATGATGAAAACTGGGGGCACGAAATAGGAAGGACACTTACAGAAAAGAGCCGAGGCCTATTTAGTGCTAATGACTGGCAG
TGTAAAACTTGCAGCAATGTGAATTTGGCCAGAATATCAGAGTGTAATTTGTGTAATACTCCAAAGTATGCTAAATTAGA
AGAAAGAAAAGGACATGGTGGAGGTTTTAATGAAAGAGGGAATGTTGAATATATTGAAAGAGAAGAATTTGATGGTGAAT
ATAATGAGTTAGGATGTAAAAAGAAAAAATAAGGAGGGAAAGCAGTTTGTCTTGCATCTATATTAATGGAATTTGAAGAT
AAAGAATCAGAGGAAGAAGGGGATGAGGATCAAGATCTTTCTAAATATAAATTAAATGAAGGTGAGGATGAAGAATCTAA
AACATGAAGTCACTCAAAGTCTCTATCTTCACATTCATGATCTTCATCATGCTCATCCTTCCCCTCAAGTTCAAGGTCTA
GGTCCAGGTCCCATTCAAGAAGTTTTTCAGTTTTTAGTCAAGATCTTATTTCAATTCCAGAGAATATTCTAGATCTTGTG
GATCAAAATCAGTATCCAGCTCCAGGTTTCACCAGGGCTTTTCTTCCCCATGAAAAAGATATTATTCAAGTTCATCATCT
CCTGAGAGGAACAGAAAGAGAAGTCATTCTAGTTTTCTTCATATGGTGATGGCAAAAAATATGAACAAGATCACAGTCAC
CCAAAATCCAGGTGATTGGTGAAAACACTAAA

Alignment

ORF - retro_cjac_2350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.56 %
• Parental protein coverage: 85.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MMKAGGT-EIGKTLAEKSRGLFSANDWQCKTCSNVNWARRSECNMCNTPKYAKLEERTGYGGGFNERENV
          MMK.GGT.EIG.TL.EKSRGLFSANDWQCKTCSNVN.AR.SECN.CNTPKYAKLEER.G.GGGFNER.NV
Retrocopy MMKTGGT<EIGRTLTEKSRGLFSANDWQCKTCSNVNLARISECNLCNTPKYAKLEERKGHGGGFNERGNV

Parental  EYIEREESDGEYDEFGRKKKKYRGKAVGPASIYLS-KYKLDEDEDEDDADLSKYNLDASEEEDSNKKKSN
          EYIEREE.DGEY.E.G.KKKK..GKAV..ASI......K..E.E...D.DLSKY.L...E.E.S...K..
Retrocopy EYIEREEFDGEYNELGCKKKK*GGKAVCLASILMEFEDKESEEEGDEDQDLSKYKLNEGEDEES---KT*

Parental  RRSRSKSRSSHSRSSSRSSSPSSSRSRSRSRSRSTS-SSQSRSRSSSRERSRSRGSKSRSSSRSHRGSSS
          ..S.S.S..SHS.SSS.SS.PSSSRSRSRS.SRS.S.S..SRS...SRE.SRS.GSKS.SSSR.H.G.SS
Retrocopy SHSKSLS--SHS*SSSCSSFPSSSRSRSRSHSRSFS<SF*SRSYFNSREYSRSCGSKSVSSSRFHQGFSS

Parental  PRKRSYSSSSSSPERNRKRSRSR-SSSSGDRKKRR-TRSRSPESTYASLNTK
          P.KR.Y.SSSSSPERNRKRS.S...SS.GD.KK...TRS.SP.......NTK
Retrocopy P*KR-YYSSSSSPERNRKRSHSS<FSSYGDGKKYE<TRSQSPKIQVIGENTK

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	0.07 RPM	39.65 RPM
SRP051959_heart	0.16 RPM	60.48 RPM
SRP051959_kidney	0.00 RPM	60.66 RPM
SRP051959_liver	0.06 RPM	44.97 RPM
SRP051959_lung	0.29 RPM	64.92 RPM
SRP051959_lymph_node	0.53 RPM	81.00 RPM
SRP051959_skeletal_muscle	0.22 RPM	54.22 RPM
SRP051959_spleen	0.32 RPM	66.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2350 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006356	2 retrocopies	retro_cjac_2350 , retro_cjac_4199,
Macaca mulatta	ENSMMUG00000017312	2 retrocopies	retro_mmul_2602, retro_mmul_2618,
Monodelphis domestica	ENSMODG00000000504	2 retrocopies	retro_mdom_1975, retro_mdom_443,
Oryctolagus cuniculus	ENSOCUG00000004640	2 retrocopies	retro_ocun_1170, retro_ocun_776,
Otolemur garnettii	ENSOGAG00000000485	4 retrocopies	retro_ogar_1274, retro_ogar_1841, retro_ogar_2843, retro_ogar_976,
Pan troglodytes	ENSPTRG00000000856	1 retrocopy	retro_ptro_3251,
Tupaia belangeri	ENSTBEG00000002316	3 retrocopies	retro_tbel_122, retro_tbel_3653, retro_tbel_4007,