RetrogeneDB ID: retro_cjac_2174

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:114462317..114463716(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000015062
• 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_2174
ATGTCATACCCAGGCTATCCCCCAACAGGCTACCCACCTTTCCCTGGATATCCTCCTGCAGGTCAGGAGTCATCTTTTCC
CCGTTCTGGTCAGTATCCTTATCCTAGTGGCTTTCCTCCAATGGGGGGGAGGTGCCTACCCACAAGGGCCAAGTGGTGGC
TATCCAGGAGCTGGAGGCTACCCTGCGCTTGGAGGTTATCCAGGCCCTGGAGGCTATCCTGGTGCCCCACAGCCAGGGGG
AGCTCCATCCTATCCCGGAGTTCCTCCAGGCTATGGATTTGGAGTCCCACCAGGTGGAGCAGGCTTTTCTGGCTATCCAC
AGCCACCCTCACAATCTTATGGAGGCGGTCCGGCACAGGTCCCACTACCTGGTGGCTTTCCTGAAGGACAGATGCCTTCC
CAGTATCCTGGAGGACAGCCTACTTACCCTAGTCAGCCTGCCGCAGTGACACAGGGCGCTCAAGGAACTATCCGACCAGT
TGCCAACTTCGATGCTATGAGAGATGCAGAAATTCTCCGTAAGGCAATGAAGGGTTTTGGGACAGACGAACAGGCGATTG
TGGATGTGGTGGCCAACCGTTCAAATGATCAGAGGCAAAAAATTAAAGCAGCATTTAAGACCTCGTATGGCAAGGATTTA
ATCAAAGATCTCAAATCAGAGTTAAGTGGAAATATGGAAGAACTGATCCTGGCCCTATTCATGCCTCCTACGTATTACGA
TGCCTGGAGCTTACGGAAAGCAATACAGGGAGCAGGAACTCAGGAACGTGTATTGATTGAAATTTTGTGCACGAGAACAA
ATCAGGAAATCCGAGAAATTGTCAGATGTTATCAGTCAGAATTTGGACGAGACCTTGAAAAGGACATTAGGTCAGATACA
TCAGGACATTTTGAATGCTTACTTGTGTCCATGTGCCAGGGAAATCGTGATGAAGACCAGAGTGTAAACCACCAAATGGC
TCAGGAAGATGCTCAGCGTCTCTATCAAGCTGGCGAGGGGAGACTAGGGACTGATGAATCTTGCTTTAACATGATCCTTG
CCACGAGAAGCTTTCCTCAGCTAAGAGCTACCATGGAGGCTTATTCCAGGATGACTAATCGAGATTTGTTAAGCAGTGTG
AGCCGTGAGTTTTCCGGATATGTGGAAAGTGGTTTGAAGACCATCTTGCAGTGTGCCCTGAACCGCCCTGCCTTCTTTGC
TGAGAGACTCTACTATGCTATGAAAGGTGCTGGTACAGATGACTCCACCCTGGTCAGGATTGTGGTCACTCGAAGTGAGA
TTGATCTTGTACAAATAAAACAAATGTTCGCTCAGATGTATCAGAAGACCCTGGGCACAATGATTGTAGGTGACACAAGT
GGAGATTACCGAAGACTTCTTCTGGCTATTGTGGGCCAG

Alignment

ORF - retro_cjac_2174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSYPGYPPTGYPPFPGYPPAGQESSFPPSGQYPFPSGFPPMGG-GAYPQVPSGGYPGAGGYPAPGGYPAP
          MSYPGYPPTGYPPFPGYPPAGQESSFP.SGQYP.PSGFPPMGG.GAYPQ.PSGGYPG.............
Retrocopy MSYPGYPPTGYPPFPGYPPAGQESSFPRSGQYPYPSGFPPMGG>GAYPQGPSGGYPGXXXXXXXXXXXXX

Parental  GGYPGAPQPGGAPSYPGVPPGHGFGVPPSGAGFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQ
          .....APQPGGAPSYPGVPPG.GFGVPP.GAGFSGYPQPPSQSYGGGPAQVPLPGGFP.GQMPSQYPGGQ
Retrocopy XXXXXAPQPGGAPSYPGVPPGYGFGVPPGGAGFSGYPQPPSQSYGGGPAQVPLPGGFPEGQMPSQYPGGQ

Parental  PTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSY
          PTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSY
Retrocopy PTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSY

Parental  GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAMQGAGTQERVLIEILCTRTNQEIREIVRCYQS
          GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKA.QGAGTQERVLIEILCTRTNQEIREIVRCYQS
Retrocopy GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAIQGAGTQERVLIEILCTRTNQEIREIVRCYQS

Parental  EFGRDLEKDIRSDTSGHFERLLVSMCQGNRDENQSVNHQMAQEDAQRLYQAGEGRLGTDESCFNMILATR
          EFGRDLEKDIRSDTSGHFE.LLVSMCQGNRDE.QSVNHQMAQEDAQRLYQAGEGRLGTDESCFNMILATR
Retrocopy EFGRDLEKDIRSDTSGHFECLLVSMCQGNRDEDQSVNHQMAQEDAQRLYQAGEGRLGTDESCFNMILATR

Parental  SFPQLRATMEAYSRMANRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGAGTDDSTLVR
          SFPQLRATMEAYSRM.NRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGAGTDDSTLVR
Retrocopy SFPQLRATMEAYSRMTNRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGAGTDDSTLVR

Parental  IVVTRSEIDLVQIKQMFAQMYQKTLGTMIAGDTSGDYRRLLLAIVGQ
          IVVTRSEIDLVQIKQMFAQMYQKTLGTMI.GDTSGDYRRLLLAIVGQ
Retrocopy IVVTRSEIDLVQIKQMFAQMYQKTLGTMIVGDTSGDYRRLLLAIVGQ

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	0.07 RPM	71.73 RPM
SRP051959_heart	0.14 RPM	50.15 RPM
SRP051959_kidney	0.24 RPM	58.28 RPM
SRP051959_liver	0.15 RPM	49.82 RPM
SRP051959_lung	0.16 RPM	48.48 RPM
SRP051959_lymph_node	0.14 RPM	49.45 RPM
SRP051959_skeletal_muscle	0.11 RPM	41.71 RPM
SRP051959_spleen	0.13 RPM	66.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2174 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2174 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,