RetrogeneDB ID: retro_cjac_1785

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:43483746..43484714(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSTA3
• Ensembl ID: ENSCJAG00000021409
• Aliases: None
• Description: tissue specific transplantation antigen P35B [Source:HGNC Symbol;Acc:12390]

Sequence

>retro_cjac_1785
ATGGAGGAACCCCAGGGGTCCATGCGGATTCTAGTGCTGGGGGCTCTGGGCTGGTGGGCAAAGCCATCCAGAAGGTGGTA
GCAGATGGAGCTGGCCTTCCTGGAGAGGACTGGGTGTTTGTCTCCTCCAAGGACGCGGATCTCAGGGATGCAGCACAGAC
CCGCCCCCTGTTTGAGAAGGTCGGACCCGCGCACATCATCCATGTTGCTGCAATGGTGGGGGGCCTGTTCTGGAATATCA
AATACAATTTGGACTTTTGGAGGAAAAATGTGCACATCAATGACAACGTCCTGCACTCCGCCTTCAAAGTGGGCACCCGC
AAGGTGGTGTCCTGCCTGTTCACTTGTATTTTCCCTGACAAGACTACCTACCTGATAGATGAGACCACATAGATGAGCCA
CAGTGGGCCGCCCCACAGCAGCAATTTTGGGTACTCATATGCCAAGAGGATGATCGACGTGCAGAACAGGGCCTACTTCC
AGCAGCACAGCTGCATGTTCACCGCTGTCATCCCCACCAACGTCTTCAGGCCCCATGACAACTTCAACATTGAGGATGGC
CAAGTGCTGCCTGGCCTCATCCACAAGGTGCACCTGGCCGAGAGCAGCGACTCGGCCCTTACGGTGTCGGGTACGGGGAA
GCCGCAGAGGCAGTTCATATACTCTCTGGACCTGGCCCAGCTCTTTATCTGGGTCCTGTGGGAGTATAGCGAGGTGGAGC
CCATCATCTTCTCAGTGGGCGAGGAAGATGAGGTCTTCATCAGGGAGGCAGCTGAGGTGGTGGTGGAGGCTATGAACTTC
CATGGGGAGGCCACCTTTGATACAACCAAGTCAGACAGGCAGTTTAAGAAGACAGCCAGTAACAGCAAGCTGAGGACCTA
CCTGCCCAACCTCCGGTTCACACCCTTCAAGCAGGCGGTGAAGGCGACCTGTGCTTGGTTCACCGACAGCTAGGAGCAGC
CCTGGAAG

Alignment

ORF - retro_cjac_1785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEPQGSMRILV-TGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTDAAQTRTLFEKVRPTHVIHL
          M.EPQGSMRILV..GGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADL.DAAQTR.LFEKV.P.H.IH.
Retrocopy MEEPQGSMRILV<AGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLRDAAQTRPLFEKVGPAHIIHV

Parental  AAMVGGLFRNIKYNLDFWRKNVHINDNVLHSAFEVGARKVVSCLSTCIFPDKTTYPIDET--MIHNGPPH
          AAMVGGLF.NIKYNLDFWRKNVHINDNVLHSAF.VG.RKVVSCL.TCIFPDKTTY.IDET..M.H.GPPH
Retrocopy AAMVGGLFWNIKYNLDFWRKNVHINDNVLHSAFKVGTRKVVSCLFTCIFPDKTTYLIDETT*MSHSGPPH

Parental  SSNFGYSYAKRMIDVQNRAYFQQHGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSSGSALTV
          SSNFGYSYAKRMIDVQNRAYFQQH.C.FTAVIPTNVF.PHDNFNIEDG.VLPGLIHKVHLA.SS.SALTV
Retrocopy SSNFGYSYAKRMIDVQNRAYFQQHSCMFTAVIPTNVFRPHDNFNIEDGQVLPGLIHKVHLAESSDSALTV

Parental  WGTGKPRRQFIYSLDLAQLVIWVLREYNEVEPIILSVGEEDEVTIREAAEAVVEAMDFHGEVTFDTTKSD
          .GTGKP.RQFIYSLDLAQL.IWVL.EY.EVEPII.SVGEEDEV.IREAAE.VVEAM.FHGE.TFDTTKSD
Retrocopy SGTGKPQRQFIYSLDLAQLFIWVLWEYSEVEPIIFSVGEEDEVFIREAAEVVVEAMNFHGEATFDTTKSD

Parental  GQFKKTASNSKLRTYLPDFRFTPFKQAVKETCAWFTDNYEQARK
          .QFKKTASNSKLRTYLP..RFTPFKQAVK.TCAWFTD..EQ..K
Retrocopy RQFKKTASNSKLRTYLPNLRFTPFKQAVKATCAWFTDS*EQPWK

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	13.56 RPM
SRP051959_heart	0.00 RPM	4.14 RPM
SRP051959_kidney	0.00 RPM	8.92 RPM
SRP051959_liver	0.00 RPM	5.05 RPM
SRP051959_lung	0.03 RPM	5.60 RPM
SRP051959_lymph_node	0.00 RPM	5.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.55 RPM
SRP051959_spleen	0.00 RPM	5.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1785 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1785 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021409	1 retrocopy	retro_cjac_1785 ,
Sarcophilus harrisii	ENSSHAG00000006859	1 retrocopy	retro_shar_225,