RetrogeneDB ID: retro_cjac_571

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82747878..82748996(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRRC2A
• Ensembl ID: ENSCJAG00000003047
• Aliases: None
• Description: proline-rich coiled-coil 2A [Source:HGNC Symbol;Acc:13918]

Sequence

>retro_cjac_571
TGTTGATCTGCTCACAGCAAGGATTCCCAGTCAGCTTCTGGTGAGGAACGGCCCCCTGAAGCAGATGGCAAAAAGGGCAA
CTCTCCCGGCAGTGAACCGCCCCCTGGCTCTGAACCTCCTAGGAGACCCCCCCTGCCCCCCACCAATGGGGACAGAAAGG
AGCTGCCCCCAGGAGCAGCCACTGCCCCCTGGCCTCATTGGCACAGAACGATCACAGCGTACAGACACAGTACCAGAGCC
TGTCCCCATTCCGCCATCTCATCGACCTGGCCCCCCTGTCCAGTTTGGCACTAGTGGCAAGGACTCAGACTTACGCCTCG
TGGTAGGAGACACCTTAAAAGCAGAGAAGGAGCTAACAGTATCAGTCACTGAGGCCATTCCTATATCCCGAGACTGGGAG
CTGCTTCCCAGTGCTGCAGCCTCTGCTGAGCCACAATCCAAGAACCTGGGTTCTGGGCACTGTGGCACAGAGCCCAGCTC
CTCAGGCCAGCGCCTATATCCTGAGGTCTTCTATGGAAGCCCTGGACCTTCCAGTTCTCAGGTCTCTGGGGGAGCCATGG
ACTCTCAATTGCATCCAAACAGTGGGGGCTTCTGCCCTGGGACACCCTCACTGCATCCTTACAGATCACAGCCCGTATAC
CTACCCCCTGGCCCAGCCCCTCCCTCAACTACTCTCTGGGGTAGCTCTCAAGAGTGAGTTTCTAGATTTCTCCACACTAC
AAGCTGCAGAGCTAGGGAAGTTGCTGGCTGGAGGAGTTCTCCACCCTCCACCTTCCTTCCTCTACTCTACAGCTTTCTGC
CCCAGTCCTTTGCCCGACATGTAGTTGCTTCAGGTACACCAGGATCTGCCATCCCCTTCGGATTTTTATTCTCCTCTGCA
GCCTGGTGGCCAAAGTGGCTTTCTCCCTTCAGGGGCTCCTGCCCAACAGATGCTTCTACCCATGATAGACTCACAGCTGC
CTGTGGTGAATTTTGGCTCCCTGCCACCAGCACCACCTCCTGCCCCACCTCCCCTTTCTCTGTTACCTGTGGGCCCTGCT
CTGCAGCCCCCCAGCCTGGCTGTGTGGCCCCCACCTGCTACTGCTCCTCGGGTGCTGCCTTCACCTGCCAGGCCCTTC

Alignment

ORF - retro_cjac_571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.16 %
• Parental protein coverage: 60.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CSQRSSPDGGLKGAAEGPPKRPGGPSPLNAVTCEGPPGSEPPRRPPPAPHDGDRKELP-REQPLPPGPIG
          C....S.D.......E.PP...G.....N....E.PPGSEPPRRPP..P..GDRKELP..EQPLPPG.IG
Retrocopy C*SAHSKDSQSASGEERPPEADGKKG--NSPGSEPPPGSEPPRRPPLPPTNGDRKELP>QEQPLPPGLIG

Parental  TERSQRTDRVPEPGPIRPSHRPGPPIQFGTSDKDSDLRLVVGDTLKAEKELSVSVTEAIPISRDWELLPS
          TERSQRTD.VPEP.PI.PSHRPGPP.QFGTS.KDSDLRLVVGDTLKAEKEL.VSVTEAIPISRDWELLPS
Retrocopy TERSQRTDTVPEPVPIPPSHRPGPPVQFGTSGKDSDLRLVVGDTLKAEKELTVSVTEAIPISRDWELLPS

Parental  AAASAEPQSKNLGSGHCGTEPSSSGQRLYPEVFYGSPGPSSSQVSGGAMDSQLHPNSGGFRPGTPSLHPY
          AAASAEPQSKNLGSGHCGTEPSSSGQRLYPEVFYGSPGPSSSQVSGGAMDSQLHPNSGGF.PGTPSLHPY
Retrocopy AAASAEPQSKNLGSGHCGTEPSSSGQRLYPEVFYGSPGPSSSQVSGGAMDSQLHPNSGGFCPGTPSLHPY

Parental  RSQPLYLPPGPAPPSALLSGVALK--GQFLDFSTLQAAELGKLPAGGVLYPPPSFL-YSTAFCP-SPLPD
          RSQP.YLPPGPAPPS..L.G........FL......A.E.....AG....PP..FL.....F.P.SPLPD
Retrocopy RSQPVYLPPGPAPPSTTLWGSSQE*VSRFLHTTSCRAREV----AGWRSSPPSTFLPLLYSFLP>SPLPD

Parental  TSLLQVRQDLPSPSDFYSPLQPGGQSGFLPSGAPAQQMLLPMVDSQLPVVNFGSLPPAPPPAPPPLSLLP
          ..LLQV.QDLPSPSDFYSPLQPGGQSGFLPSGAPAQQMLLPM.DSQLPVVNFGSLPPAPPPAPPPLSLLP
Retrocopy M*LLQVHQDLPSPSDFYSPLQPGGQSGFLPSGAPAQQMLLPMIDSQLPVVNFGSLPPAPPPAPPPLSLLP

Parental  VGPALQPPSLAVRPPPAPAPRVLPSPARPF
          VGPALQPPSLAV.PPPA.APRVLPSPARPF
Retrocopy VGPALQPPSLAVWPPPATAPRVLPSPARPF

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	15.29 RPM
SRP051959_heart	0.02 RPM	29.57 RPM
SRP051959_kidney	0.00 RPM	18.73 RPM
SRP051959_liver	0.00 RPM	6.28 RPM
SRP051959_lung	0.02 RPM	19.85 RPM
SRP051959_lymph_node	0.00 RPM	22.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	17.19 RPM
SRP051959_spleen	0.00 RPM	18.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_571 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003047	2 retrocopies	retro_cjac_571 , retro_cjac_572,