RetrogeneDB ID: retro_cjac_3730

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01197383.1:2946..3573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000037656
• Aliases: None
• Description: None

Sequence

>retro_cjac_3730
TCCTCCTTCTGCCTGCAGGTTAACATGGCTGCAGCACAGCGTCATCACTGCTCAGCATTGCCCTGCTCACCCTACCTCAT
GGCTGACCCTTCAGGACCACTGATGGCTTGCCCGCCACCTCCTCCATTTGGGTGTCGCCTGGGAGCTCCACCATTCCCAT
CAGCTAAAGGTGTTCTGGGACCTCTGACAACTCCTCGACTCCAATGTCCACTAGACACAGACACCTACACCCGCATGTCT
TCTGGCTGCTTTACCACCTTAGCCAATGATTTTCTGAGCTTATACACAATTCCACCTGAGTGTCTATGCACACCTCTGCC
AGCTTCGTCAGATGATGAGTTCTCGAGACCACAGACACCTACACCTGAATGTCTTCTGGCTGCTTTACCACCTTCTTCAG
CCAATGATTTTCTGAGCTTATACACAATTCCACCTGAGTGTCTATGCACACCTCTGCCAGCTTCGTCAGATGATGAGTTC
TCGAGACCACAGACACCTACACCTGAATGTCTTCTGGCAGCTTTACCACCTTCTTCAGCCAATGATTTCCTTGGCTTATA
CACAATTCCACCTGAGTGTCTATGCACGCCTCTGCCAGCTTCGTCAGATGATGAGTTCTCGAGACCA

Alignment

ORF - retro_cjac_3730 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSFCLQVNMAAAQHHHCSALPSSPYLMADRSRPLMACQPPPPSGCHPVANDFLSSYTTPKCLLTP-LPPP
          SSFCLQVNMAAAQ.HHCSALP.SPYLMAD.S.PLMAC.PPPP.GC...A..F.S.......L.TP.L..P
Retrocopy SSFCLQVNMAAAQRHHCSALPCSPYLMADPSGPLMACPPPPPFGCRLGAPPFPSAKGVLGPLTTPRLQCP

Parental  TD-DEFSRPQTLTHECLLAPAEDFLGPDTPPPECLLTPLPPSTDDEFSRP----PKCLLTPLPPSTDDEF
          .D.D...R.......C....A.DFL...T.PPECL.TPLP.S.DDEFSRP....P.CLL..LPPS....F
Retrocopy LDTDTYTR---MSSGCFTTLANDFLSLYTIPPECLCTPLPASSDDEFSRPQTPTPECLLAALPPSSANDF

Parental  LRPQTLTHECLLAPVPPAPHDNLWRPWSPPPKCLLTYLPPSTDDEFSRPQMLTYECLLAPVPPAPHDNLW
          L...T...ECL..P.P....D...RP..P.P.CLL..LPPS....F........ECL..P.P....D...
Retrocopy LSLYTIPPECLCTPLPASSDDEFSRPQTPTPECLLAALPPSSANDFLGLYTIPPECLCTPLPASSDDEFS

Parental  RP
          RP
Retrocopy RP

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	0.16 RPM	0.00 RPM
SRP051959_heart	0.05 RPM	0.00 RPM
SRP051959_kidney	0.18 RPM	0.00 RPM
SRP051959_liver	0.13 RPM	0.02 RPM
SRP051959_lung	0.07 RPM	0.00 RPM
SRP051959_lymph_node	0.07 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.00 RPM
SRP051959_spleen	0.08 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3730 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3730 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000037656	1 retrocopy	retro_cjac_3730 ,