RetrogeneDB ID: retro_cjac_1004

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:107431317..107432124(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSCJAG00000018514
• Aliases: None
• Description: RAD1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9806]

Sequence

>retro_cjac_1004
AAGTACAGCCTTTTGGCCAGCCTTGACCACGTTAGGAATCTCTCTGCCATCTTGAAAGCTGTTCATTTCCGAAAATATGC
CACGTGTTTTGCAACTAAAAATGGAATCAAAGTAACAGTGAAAAATACAAAGTGTGTGCAAGCAAATGCTTTTATTCAGG
CTGGAATATTTCAAGACTTTAGAGTTCAGGAAGAGTCTGTTACTTTTCAAATTCATTTAACTGTCCTTTTAGACTGTTGA
CGTATTTTTGGATCAAGTCCTATACCAGGGACTTGAAGTGCACTTCCGATGTGTTACCAAGGTTATGGTCACCCTTTGAT
GCCGTTCCTGGAGAAGGAGGAGTGGTGGCAGTCTCCAAAATCAATAAGCAGGAACCCGAGGAGACTCAGGACTTTTATTT
CTGCAGCACCAATGTTATTAATAAAATTATTCTGCAGTCAGAAGGGCTCCGTGAAGCCGTTTTCTGAATTGGGTATGATA
AATGAAGTCCTACAAATTACCAGGTCTCCTGACAAGCCTTATTTCAGGTTATCTACTTTTGTAAATGCAGGAAGTTCCCA
CCTTGACTGTCCCAAAGATTCTGATTTAATGGAAGCATTTCATTGTATTCAGACCCAAGTCAACAGCTACAAGATTTCCT
TACTGAAATCCTCTACAAAGGCGGTAGTTCTGTCTTGTAAGCTATCTATTTGGACAGATAACCAAGGCTTTCTTTCATTA
CATTATATGATTAGAAATTAAGATAGACAAATAAGTTTTGTGGAATACTACTGCTGCCCTGATGAAGAAGTTCCTGAATC
TGAGTCT

Alignment

ORF - retro_cjac_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 95.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QYSLVASLDNVRNLSTILKAIHFREHATCFATKNGIKVTVENAKCVQANAFIQAGIFQEFKVQEESVTFR
          .YSL.ASLD.VRNLS.ILKA.HFR..ATCFATKNGIKVTV.N.KCVQANAFIQAGIFQ.F.VQEESVTF.
Retrocopy KYSLLASLDHVRNLSAILKAVHFRKYATCFATKNGIKVTVKNTKCVQANAFIQAGIFQDFRVQEESVTFQ

Parental  INLTVLLDCLSIFGSSPMPGTLTALRMCYQGDGYPLMLFLE-EGGVVTVCKINTQEPEETLDFDFCSTNV
          I.LTVLLDC..IFGSSP.PGT..AL.MCYQG.G.PLM.FLE.EGGVV.V.KIN.QEPEET.DF.FCSTNV
Retrocopy IHLTVLLDC*RIFGSSPIPGT*SALPMCYQGYGHPLMPFLE<EGGVVAVSKINKQEPEETQDFYFCSTNV

Parental  INKIILQSEGLREA-FSELDMTSEVLQITMSPDKPYFRLSTFGNAGSSHLDYPKDSDLMEAFHCNQTQVN
          INKIILQSEGLREA.FSEL.M..EVLQIT.SPDKPYFRLSTF.NAGSSHLD.PKDSDLMEAFHC.QTQVN
Retrocopy INKIILQSEGLREA>FSELGMINEVLQITRSPDKPYFRLSTFVNAGSSHLDCPKDSDLMEAFHCIQTQVN

Parental  RYKISLLKPSTKALVLSCKVSIRTDNRGFLSLQYMIRNEDGQICFVEYYCCPDEEVPESES
          .YKISLLK.STKA.VLSCK.SI.TDN.GFLSL.YMIRN.D.QI.FVEYYCCPDEEVPESES
Retrocopy SYKISLLKSSTKAVVLSCKLSIWTDNQGFLSLHYMIRN*DRQISFVEYYCCPDEEVPESES

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	2.68 RPM
SRP051959_heart	0.09 RPM	2.95 RPM
SRP051959_kidney	0.04 RPM	2.60 RPM
SRP051959_liver	0.00 RPM	2.10 RPM
SRP051959_lung	0.00 RPM	3.69 RPM
SRP051959_lymph_node	0.02 RPM	4.82 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.41 RPM
SRP051959_spleen	0.04 RPM	3.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1004 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1004 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_634
Pan troglodytes	retro_ptro_462
Gorilla gorilla	retro_ggor_555
Pongo abelii	retro_pabe_564

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018514	1 retrocopy	retro_cjac_1004 ,
Homo sapiens	ENSG00000113456	1 retrocopy	retro_hsap_634,
Gorilla gorilla	ENSGGOG00000004219	1 retrocopy	retro_ggor_555,
Macaca mulatta	ENSMMUG00000030184	1 retrocopy	retro_mmul_54,
Nomascus leucogenys	ENSNLEG00000014437	1 retrocopy	retro_nleu_455,
Otolemur garnettii	ENSOGAG00000014822	2 retrocopies	retro_ogar_2296, retro_ogar_2726,
Pongo abelii	ENSPPYG00000015389	1 retrocopy	retro_pabe_564,
Pan troglodytes	ENSPTRG00000016783	1 retrocopy	retro_ptro_462,
Tarsius syrichta	ENSTSYG00000002894	1 retrocopy	retro_tsyr_738,