RetrogeneDB ID: retro_cjac_561

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81426985..81427671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TGFB2
• Ensembl ID: ENSCJAG00000012931
• Aliases: None
• Description: None

Sequence

>retro_cjac_561
AGCACACTCGATATGGACCAGTTCATGCGCAAGAGGATCGAGGCGATCCGCGGGCAGATCCTGAGCAAGCTGAAGCTTAC
CAGACCCCCAGAAGACTATCCTGAGCCCGAGGAAGTCCCCCCGGAGGTGATTTCCATCTACAACAGCACCAGGGACTTGT
CCAGGAGAAGGTGAGCCGGAGGCCTGCCACCTGCAAGCGCGAGAGGAGCGACGAGGAGTACTACGCCAAGGAGGTTTACA
AAATAGACACGCCGCCCTTCTTCCCCTCCGAAAATGCCATCCCGCCCACTTTCTACAGACCCGACTTCAGAATTGTCCGA
TTTGATGTCTCAGCAATGGAGAAGAATGCTTCCAATTTGGTGAAAGCAGAGTTCAGAGTCTTTCGTTTGCAGAACCCAAA
AGCCAGAGTGCCTGAACAACGGATCGAGCTGTATCAGATTCTCAAGTCCAAAGATTGAACATCTCTAACCCAGCGCTACA
TCAACAGCAAAGTTGTGAAAACAAGAGCAGAAGGCGAATGGTTCTCTTTTGATGTAACTGATGCTGTTCATGAATGGCTT
CACCATAAAGACAGGAATCTGGGGTTTAAAATAAGCTTACACTGTCCCTGTTGTACTTTTGTACCATCTAATAATTACAT
CATCCCAAATAAAAGCGAAGAACTAGAAGCAAGATTTGCAGACTTG

Alignment

ORF - retro_cjac_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.48 %
• Parental protein coverage: 55.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STLDMDQFMRKRIEAIRGQILSKLKLTSPPEDYPEPEEVPPEVISIYNSTRDL-LQEKASRRAAACERER
          STLDMDQFMRKRIEAIRGQILSKLKLT.PPEDYPEPEEVPPEVISIYNSTRDL..QEK.SRR.A.C.RER
Retrocopy STLDMDQFMRKRIEAIRGQILSKLKLTRPPEDYPEPEEVPPEVISIYNSTRDL<VQEKVSRRPATCKRER

Parental  SDEEYYAKEVYKIDMPPFFPSENAIPPTFYRPYFRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPE
          SDEEYYAKEVYKID.PPFFPSENAIPPTFYRP.FRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPE
Retrocopy SDEEYYAKEVYKIDTPPFFPSENAIPPTFYRPDFRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPE

Parental  QRIELYQILKSKDLTSPTQRYIDSKVVKTRAEGEWLSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVP
          QRIELYQILKSKD.TS.TQRYI.SKVVKTRAEGEW.SFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVP
Retrocopy QRIELYQILKSKD*TSLTQRYINSKVVKTRAEGEWFSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVP

Parental  SNNYIIPNKSEELEARFAGI
          SNNYIIPNKSEELEARFA..
Retrocopy SNNYIIPNKSEELEARFADL

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	3.90 RPM
SRP051959_heart	0.00 RPM	16.38 RPM
SRP051959_kidney	0.00 RPM	7.52 RPM
SRP051959_liver	0.00 RPM	1.00 RPM
SRP051959_lung	0.00 RPM	9.19 RPM
SRP051959_lymph_node	0.00 RPM	1.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.90 RPM
SRP051959_spleen	0.00 RPM	2.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_561 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_561 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	ENSCJAG00000012931	1 retrocopy	retro_cjac_561 ,