RetrogeneDB ID: retro_cjac_1471

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:50905987..50906298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf49
• Ensembl ID: ENSCJAG00000009570
• Aliases: None
• Description: chromosome 12 open reading frame 49 [Source:HGNC Symbol;Acc:26128]

Sequence

>retro_cjac_1471
TGGGTATGTGGGGCCCTTGCCCAGGCTGTCCTCGTCCATGTCCTCAGCAGCACCTTCTGGCAGGAAGAGAGGGAGTGAGA
TGTAGGACTCTCCTCCAGGTTCAAGACCATGACCAGCCCATCCTGTGGAACGTGCAGTTTAACCTGGGCAGTAGCAGTCA
CCCAAGCAATCAGTGACAGAACTCTGTTCAAGAGAAGCTCCTCATCACAGATGAACCAGGTAATATTTGTGAGAGGACGG
ATTTGCTGGTGAAAGGTTGTAATGTCCACATCCCTAGCGCAAAGCAGTACTGCTGTGATGTCTGCTGACCG

Alignment

ORF - retro_cjac_1471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.98 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WVLALVFGLSLVYFLSSTFKHEER-AVRDRNLLQVQDHDQPILWKVQFNLGNSSRPSNQCRNSIQGKHLI
          WV........LV..LSSTF..EER..VR.R.LLQVQDHDQPILW.VQFNLG.SS.PSNQ..NS.Q.K.LI
Retrocopy WVCGALAQAVLVHVLSSTFWQEER<GVRCRTLLQVQDHDQPILWNVQFNLGSSSHPSNQ*QNSVQEKLLI

Parental  TDELGYVCERKDLLVNGCCNVNVPSTKQYCCDGCWP
          TDE.G..CER.DLLV.G.CNV..PS.KQYCCD.C.P
Retrocopy TDEPGNICERTDLLVKG-CNVHIPSAKQYCCDVC*P

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	0.20 RPM	11.12 RPM
SRP051959_heart	0.05 RPM	6.10 RPM
SRP051959_kidney	0.07 RPM	12.22 RPM
SRP051959_liver	0.02 RPM	4.96 RPM
SRP051959_lung	0.10 RPM	11.86 RPM
SRP051959_lymph_node	0.00 RPM	8.01 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.63 RPM
SRP051959_spleen	0.02 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1471 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1471 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2798
Macaca mulatta	retro_mmul_2376

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012481	2 retrocopies	retro_amel_1518, retro_amel_1578,
Bos taurus	ENSBTAG00000047139	1 retrocopy	retro_btau_1667,
Callithrix jacchus	ENSCJAG00000009570	1 retrocopy	retro_cjac_1471 ,
Dasypus novemcinctus	ENSDNOG00000001294	9 retrocopies	retro_dnov_126, retro_dnov_1532, retro_dnov_1609, retro_dnov_1622, retro_dnov_1739, retro_dnov_2042, retro_dnov_2185, retro_dnov_2285, retro_dnov_232,
Echinops telfairi	ENSETEG00000016892	3 retrocopies	retro_etel_1064, retro_etel_1377, retro_etel_410,
Homo sapiens	ENSG00000111412	1 retrocopy	retro_hsap_4758,
Gorilla gorilla	ENSGGOG00000015690	2 retrocopies	retro_ggor_2963, retro_ggor_508,
Myotis lucifugus	ENSMLUG00000011912	1 retrocopy	retro_mluc_166,
Macaca mulatta	ENSMMUG00000018247	2 retrocopies	retro_mmul_2376, retro_mmul_2537,
Pan troglodytes	ENSPTRG00000005500	1 retrocopy	retro_ptro_2798,