RetrogeneDB ID: retro_cjac_860

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:71136538..71137546(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022250
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001720
• Aliases: None
• Description: Annexin [Source:UniProtKB/TrEMBL;Acc:F6XT66]

Sequence

>retro_cjac_860
ATGCCTTCTCAGTATCCTGGAGGACAGCCTACTTACCCTAGTCAGCCTGCCGCAGTGACTCAGGGCGCTCAAGGAACTAT
CCGACCAGTTGCCGACTTCGATGCTATGAGAGATGCAGAAATTCTCCGTAAGGCAATGAAGGGTTTTGGGACAGACGAAC
AGGCGATTGTGGATGTGGTGGCCAACCGTTCCAATGATAAGAGGCAAAAAATTAAAGCAGCATTTAAGACCTCGAATGGC
AAGGATTTAATCAAAGATCTCAAATCAGAGTTAAGTGGAAATATGGAAGAACTGATCCTGGCCCTATTCATGCCTCCTAC
GTATTACGATGCCTGGAGCTTACGGAAAGCAGTGCAGGGAGCAGGAACTCAGGAACGTGTATTGATTGAAATTTTGTGCA
CGAGAACAAATCAGGAAATCCGAGAAATTGTCAGATGTTATCAGTCAGAATTTGGACGAGACCTTGAAAAGGACATTAGG
TCAGATACATCAGGACATTTTGAACGCTTACTTGTGTCCACGTGCCAGGGAAATCGTGATGAAAACCAGAGTGTAAACCA
CCAAATGGCTCAGGAAGATGCTCAGCGTCTCTATCAAGCTGGTGAGGGGAGACTAGGGACTGATGAATCTTGCTTTAACA
TGATCCTTGCCACGAGAAGCTTTCCTCAGCTAAGAGCTACCATGGAGGCTTATTCCAGGATGGCTAATCGAGATTTGTTA
AGCAGTGTGAGCCGTGAGTTTTCCAGATATGTGGAAAGTGGTTTGAAGACCATCTGGCAGTGTGCCCTGAACCGCCCTGC
CTTCTTTGCTGAGAGGCTCTACTATGCTATGAAAGGTGCTGGTACAGATGACTCCACCCTGGTCAGGATTGTGGTCACTC
GAAGTGAGATTGATCTTGTACAAATAAAACAAATGTTCTCTCAGATGTATCAGAAGACCCTGGGCACAATGATTGCAGGT
GACACGAGTGGAGATTACCAAAGACTTCTTCTGGCTATTGTGGGCCAG

Alignment

ORF - retro_cjac_860 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSQYPGGQPTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQK
          MPSQYPGGQPTYPSQPAAVTQGAQGTIRPVA.FDAMRDAEILRKAMKGFGTDEQAIVDVVANRSND.RQK
Retrocopy MPSQYPGGQPTYPSQPAAVTQGAQGTIRPVADFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDKRQK

Parental  IKAAFKTSYGKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAMQGAGTQERVLIEILCTRTNQEI
          IKAAFKTS.GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKA.QGAGTQERVLIEILCTRTNQEI
Retrocopy IKAAFKTSNGKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAVQGAGTQERVLIEILCTRTNQEI

Parental  REIVRCYQSEFGRDLEKDIRSDTSGHFERLLVSMCQGNRDENQSVNHQMAQEDAQRLYQAGEGRLGTDES
          REIVRCYQSEFGRDLEKDIRSDTSGHFERLLVS.CQGNRDENQSVNHQMAQEDAQRLYQAGEGRLGTDES
Retrocopy REIVRCYQSEFGRDLEKDIRSDTSGHFERLLVSTCQGNRDENQSVNHQMAQEDAQRLYQAGEGRLGTDES

Parental  CFNMILATRSFPQLRATMEAYSRMANRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGA
          CFNMILATRSFPQLRATMEAYSRMANRDLLSSVSREFS.YVESGLKTI.QCALNRPAFFAERLYYAMKGA
Retrocopy CFNMILATRSFPQLRATMEAYSRMANRDLLSSVSREFSRYVESGLKTIWQCALNRPAFFAERLYYAMKGA

Parental  GTDDSTLVRIVVTRSEIDLVQIKQMFAQMYQKTLGTMIAGDTSGDYRRLLLAIVGQ
          GTDDSTLVRIVVTRSEIDLVQIKQMF.QMYQKTLGTMIAGDTSGDY.RLLLAIVGQ
Retrocopy GTDDSTLVRIVVTRSEIDLVQIKQMFSQMYQKTLGTMIAGDTSGDYQRLLLAIVGQ

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	0.04 RPM	71.73 RPM
SRP051959_heart	0.18 RPM	50.15 RPM
SRP051959_kidney	0.20 RPM	58.28 RPM
SRP051959_liver	0.06 RPM	49.82 RPM
SRP051959_lung	0.16 RPM	48.48 RPM
SRP051959_lymph_node	0.07 RPM	49.45 RPM
SRP051959_skeletal_muscle	0.07 RPM	41.71 RPM
SRP051959_spleen	0.08 RPM	66.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_860 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_860 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014749	1 retrocopy	retro_cfam_1107,
Callithrix jacchus	ENSCJAG00000001720	3 retrocopies	retro_cjac_1288, retro_cjac_2174, retro_cjac_860 ,
Microcebus murinus	ENSMICG00000013143	2 retrocopies	retro_mmur_404, retro_mmur_884,
Pteropus vampyrus	ENSPVAG00000013001	1 retrocopy	retro_pvam_1365,
Rattus norvegicus	ENSRNOG00000007136	1 retrocopy	retro_rnor_2446,
Ictidomys tridecemlineatus	ENSSTOG00000012433	1 retrocopy	retro_itri_1796,