RetrogeneDB ID: retro_cjac_3130

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:38195423..38196214(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNMTL1
• Ensembl ID: ENSCJAG00000021701
• Aliases: None
• Description: None

Sequence

>retro_cjac_3130
AAGAAGTTGCTAGTCGATGAGCTCACAGGTGTCAGCTTCCTTAAAGTGAAATTCAAGGACATCAAGGATTGGTCCAACCT
AGTAATGCCGTGAGAATAATGGGGATTTTTGCCAAACCTGACCATATTAACATGACATATTCAAAGACTCAGCTTTAGCA
TTCACTGACTCTATTATTGATTTGTGACAATCTTTGTGACCCTGGGAGCCTGGGGACAATTCTGAAATCTCCCACTTGGA
CAGGCTACAGCAAAGTGTTTCAAACTTTGAAAGGCTGTGTGGATGCCTGGGAGCCCAAAGTGCTACAGGTGGGTATGGGT
GCACGTTTTCAGGTACCCAGTATCAATAATCTGAAAGCAGAAATAGTGCCACATTACTTGCCCCCTGACACCCAGGTCTA
TGTGGCTGACAACTAAAACCTTTATGCTCAGGCTCAGATGTCTAATAAAGCCAGTGACTATGGCTTGGTGTATGATTGGC
GACACCTGAAGTTTCACGAGTACGAAGAAAAGTAAGGTCTAGACACTGGAGCCAGTAAAGGTTGGCTGCCTGATACTGAA
GTTCAGAGTCATGACTTGGACTGGACAGAGGCACCAGCAGCTGTGGTGGTTGGCAGCGAGACCCACGGCATGAGTCTGGA
GTCTCTGTAGTTGGCTGAGAGCACTGGGAGCAAGAGGCTGCTGATCCCTGTTGCCCCTGTTGTGAACGGTCTCAACCCAG
CCATGGCTGCACGCAACCTGCTTTTTGAAGGGAAGAGACAATTGTGGGTGAGGGTGGAACATTTAAGCAGG

Alignment

ORF - retro_cjac_3130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.32 %
• Parental protein coverage: 62.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KELPVDKLKGVSLIKVKFEDIKDWSDLVTP-QGIMGIFAKPDHVKMTYPKTQLQHSLPLLLICDNLRDPG
          K.L.VD.L.GVS..KVKF.DIKDWS.LV.P...IMGIFAKPDH..MTY.KTQL.HSL.LLLICDNL.DPG
Retrocopy KKLLVDELTGVSFLKVKFKDIKDWSNLVMP<VRIMGIFAKPDHINMTYSKTQL*HSLTLLLICDNLCDPG

Parental  NLGTILRSAAGAGCSKVLLT-KGCVDAWEPKVLRAGMSAHFQVPIINNLEWETVPNYLPPDTRIYVADNC
          .LGTIL.S....G.SKV..T.KGCVDAWEPKVL..GM.A.FQVP.INNL..E.VP.YLPPDT..YVADN.
Retrocopy SLGTILKSPTWTGYSKVFQTLKGCVDAWEPKVLQVGMGARFQVPSINNLKAEIVPHYLPPDTQVYVADN*

Parental  GRYAQAQVSNKAGDHGWVCDQRALKSHRYEEEEDVETGASQDWLPEVEVQSYDLDWTEAPAAVVVGGETH
          ..YAQAQ.SNKA.D.G.V.D.R.LK.H.YEE.....TGAS..WLP..EVQS.DLDWTEAPAAVVVG.ETH
Retrocopy NLYAQAQMSNKASDYGLVYDWRHLKFHEYEEK*GLDTGASKGWLPDTEVQSHDLDWTEAPAAVVVGSETH

Parental  GVSLESLQLAESTGGKRLLIPVVPGVDSLNSAMAASILLFEGRRQLRVRAEHLHR
          G.SLESL.LAESTG.KRLLIPV.P.V..LN.AMAA..LLFEG.RQL.VR.EHL.R
Retrocopy GMSLESL*LAESTGSKRLLIPVAPVVNGLNPAMAARNLLFEGKRQLWVRVEHLSR

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	3.15 RPM
SRP051959_heart	0.00 RPM	4.14 RPM
SRP051959_kidney	0.00 RPM	3.90 RPM
SRP051959_liver	0.00 RPM	3.96 RPM
SRP051959_lung	0.00 RPM	4.33 RPM
SRP051959_lymph_node	0.00 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.87 RPM
SRP051959_spleen	0.00 RPM	4.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3130 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3130 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3704
Gorilla gorilla	retro_ggor_2505
Pongo abelii	retro_pabe_3149
Macaca mulatta	retro_mmul_1709

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021701	1 retrocopy	retro_cjac_3130 ,
Homo sapiens	ENSG00000171861	1 retrocopy	retro_hsap_3704,
Gorilla gorilla	ENSGGOG00000015518	1 retrocopy	retro_ggor_2505,
Macaca mulatta	ENSMMUG00000011423	1 retrocopy	retro_mmul_1709,
Nomascus leucogenys	ENSNLEG00000000570	1 retrocopy	retro_nleu_180,
Pongo abelii	ENSPPYG00000007762	1 retrocopy	retro_pabe_3149,