RetrogeneDB ID: retro_cjac_1288

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:61035082..61035823(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_1288
CATACAGGCTATCCCCCAACAGGCTACGCACCTTTCCCTGGATATCCTCCTGCAGGTCAGGAGTCATCTTTTCCCCCTTC
TGGTCAGTATCCTTATCCTAGTGGCTTTCCTCCAATGTGGGGAGGTGCCTACCCACAAGTGCCAAGTAGTGGCTATCCAG
GAGCTGGAGGCAACCCTGCACCTGGAGGTTATCCAGCCCCTGGAGGCTATCCTGGTGCCCCACAGCCAGGGGGAGCTCCA
TCCTATCCTGGAGTTTCTCCAGGCCATGGATTTGGAGTCCCACCAGGTGGAGCAGACTTTTCTGGCTATCCACAGCCACC
TTCACAGTCTTATGGAGGTGGTCCAGCACAGGTCCCACTACCTGGTGGTTTTCCTGGAGGACAGATGCCTTCTCAGTATC
CTGGAGGACAGCCTACTTACCCTAGTCGGCCTGCCACAATGACTCAGGGCACTCAAGTAACTATCCAACCAGCTGCCAAC
TTCAACGCTATGAGAGATACAGAAATTCTCCATAAGGCAATGAAGCGTTTTGGGACAGACGAGCAGGCAATTGTGGATGT
GGTGGCCAACTGTTCCAATGATCAGAGGCAAAAAATTAAAGCAGCATTAAAGACCTCGTATGGCAAGGATTTGATCAAAG
ATCTCAAATTAGAATTAAGTGGAAATATGGAAGAACTGATCCTGGCCCTATTCATGACTCCTACATATTATGATGCCTGG
AGCTTACGAAAAGCAATGCAG

Alignment

ORF - retro_cjac_1288 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 53.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPGYPPTGYPPFPGYPPAGQESSFPPSGQYPFPSGFPPMGGGAYPQVPSGGYPGAGGYPAPGGYPAPGGY
          ..GYPPTGY.PFPGYPPAGQESSFPPSGQYP.PSGFPPM.GGAYPQVPS.GYPG................
Retrocopy HTGYPPTGYAPFPGYPPAGQESSFPPSGQYPYPSGFPPMWGGAYPQVPSSGYPGXXXXXXXXXXXXXXXX

Parental  PGAPQPGGAPSYPGVPPGHGFGVPPSGAGFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQPTY
          ..APQPGGAPSYPGV.PGHGFGVPP.GA.FSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQPTY
Retrocopy XXAPQPGGAPSYPGVSPGHGFGVPPGGADFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQPTY

Parental  PSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSYGKD
          PS.PA..TQG.Q.TI.P.ANF.AMRD.EIL.KAMK.FGTDEQAIVDVVAN.SNDQRQKIKAA.KTSYGKD
Retrocopy PSRPATMTQGTQVTIQPAANFNAMRDTEILHKAMKRFGTDEQAIVDVVANCSNDQRQKIKAALKTSYGKD

Parental  LIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAMQ
          LIKDLK.ELSGNMEELILALFM.PTYYDAWSLRKAMQ
Retrocopy LIKDLKLELSGNMEELILALFMTPTYYDAWSLRKAMQ

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	0.11 RPM	71.73 RPM
SRP051959_heart	0.35 RPM	50.15 RPM
SRP051959_kidney	0.20 RPM	58.28 RPM
SRP051959_liver	0.09 RPM	49.82 RPM
SRP051959_lung	0.05 RPM	48.48 RPM
SRP051959_lymph_node	0.14 RPM	49.45 RPM
SRP051959_skeletal_muscle	0.28 RPM	41.71 RPM
SRP051959_spleen	0.21 RPM	66.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1288 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1288 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,