RetrogeneDB ID: retro_cjac_1515

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:46798376..46798906(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021144
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000031971
• Aliases: None
• Description: None

Sequence

>retro_cjac_1515
GGCACAGCTAAGGCAGACAGCGGCAGCGGAGCCGGCCAGGCCTCTGCCAGGGAAGCGACAGGCGCTACTGGGGACAGTGG
CCCCATCAACCCAGCCTTGCTATCTCCCGGCGACCTGCAACTCATCACTCTCATCGTTGGAGCAGCTCAAGAGCCCTGGC
CTTTTTTGACAGCTTCCACCGGGACTGCCTGGCCGATGTGGACACAAAGCCAGCTTACCAAAACCTGAGGCAGAAAGTAG
ATAATTTTGTGTCAACGTATCTGGACAAGCAGGAATGGAATCCTACAATGATCAAAAGCCAGTTGCAAAATGGTCTGAGG
CAGAGTGTGGTTCAGTCAGGGATGTTGGAAGCTGGAGTAGAGAGGATTATTTCTCAGGTGGTGGATCCAAAACTAAACCA
CATCTTCAGGCCACAAATAGAACCAGCAATTCATGAGTTCCTGGCCGCCCAGGAAAAAAAGCAGCTGTGCCAGCACCCCC
CTCCAGAGCTTGAAGGCCAGGACCCACCAGCTCCATCTCAGGACACTTCC

Alignment

ORF - retro_cjac_1515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.22 %
• Parental protein coverage: 96.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGTGAVGGGGAGQASAGAATGATGASGGGGPINPASLPPGDPQLIALIV-EQLKSRGLF-DSFRRDCLAD
          G...A..G.GAGQASA..ATGATG.S...GPINPA.L.PGD.QLI.LIV.EQLKS.GLF.DSF.RDCLAD
Retrocopy GTAKADSGSGAGQASAREATGATGDS---GPINPALLSPGDLQLITLIV>EQLKSPGLF>DSFHRDCLAD

Parental  VDTKPAYQNLRQKVDNFVSTHLDKQEWNPTMNKNQLRNGLRQSVVQSGMLEAGVDRIISQVVDPKLNHIF
          VDTKPAYQNLRQKVDNFVST.LDKQEWNPTM.K.QL.NGLRQSVVQSGMLEAGV.RIISQVVDPKLNHIF
Retrocopy VDTKPAYQNLRQKVDNFVSTYLDKQEWNPTMIKSQLQNGLRQSVVQSGMLEAGVERIISQVVDPKLNHIF

Parental  RPQIERAIHEFLAAQ-KKAAVPAPPPEPDGQDPPAPSQDTS
          RPQIE.AIHEFLAAQ.KK.....PPPE..GQDPPAPSQDTS
Retrocopy RPQIEPAIHEFLAAQEKKQLCQHPPPELEGQDPPAPSQDTS

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	0.02 RPM	4.77 RPM
SRP051959_heart	0.02 RPM	7.00 RPM
SRP051959_kidney	0.20 RPM	8.16 RPM
SRP051959_liver	0.00 RPM	6.58 RPM
SRP051959_lung	0.05 RPM	6.07 RPM
SRP051959_lymph_node	0.02 RPM	4.38 RPM
SRP051959_skeletal_muscle	0.09 RPM	6.66 RPM
SRP051959_spleen	0.11 RPM	5.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1515 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1515 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034598	1 retrocopy	retro_btau_663,
Canis familiaris	ENSCAFG00000016776	1 retrocopy	retro_cfam_1374,
Callithrix jacchus	ENSCJAG00000031971	4 retrocopies	retro_cjac_1154, retro_cjac_1515 , retro_cjac_1536, retro_cjac_953,
Homo sapiens	ENSG00000145919	3 retrocopies	retro_hsap_102, retro_hsap_1867, retro_hsap_993,
Gorilla gorilla	ENSGGOG00000010925	2 retrocopies	retro_ggor_1365, retro_ggor_794,
Microcebus murinus	ENSMICG00000002626	1 retrocopy	retro_mmur_1126,
Macaca mulatta	ENSMMUG00000013793	2 retrocopies	retro_mmul_803, retro_mmul_869,
Mus musculus	ENSMUSG00000044502	1 retrocopy	retro_mmus_3661,
Nomascus leucogenys	ENSNLEG00000000476	1 retrocopy	retro_nleu_1224,
Oryctolagus cuniculus	ENSOCUG00000014283	1 retrocopy	retro_ocun_1071,
Otolemur garnettii	ENSOGAG00000001107	3 retrocopies	retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii	ENSPPYG00000016057	2 retrocopies	retro_pabe_1567, retro_pabe_1587,
Pan troglodytes	ENSPTRG00000017544	2 retrocopies	retro_ptro_1282, retro_ptro_757,
Ictidomys tridecemlineatus	ENSSTOG00000013505	1 retrocopy	retro_itri_1164,
Tupaia belangeri	ENSTBEG00000014046	1 retrocopy	retro_tbel_3451,
Tarsius syrichta	ENSTSYG00000007617	1 retrocopy	retro_tsyr_818,
Tursiops truncatus	ENSTTRG00000000384	2 retrocopies	retro_ttru_1004, retro_ttru_457,
Vicugna pacos	ENSVPAG00000004260	1 retrocopy	retro_vpac_452,