RetrogeneDB ID: retro_ptro_2798

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:142666107..142666418(-)
• Located in intron of: ENSPTRG00000020669

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf49
• Ensembl ID: ENSPTRG00000005500
• Aliases: None
• Description: chromosome 12 open reading frame 49 [Source:HGNC Symbol;Acc:26128]

Sequence

>retro_ptro_2798
TGGGCACGTGGGGCCCTTGCCCAGGCTATCCTCATCCACGTCCTCAGCAGCACCTTCAGGCAGGAAGAGCGGGAGTCAGA
CATAGGACTCTCCTCCAGGTTCAAGACCACGACCAGCCCAGCCCGTGCAAAGTGCAGGTTAACCTGGGCAGTAGCAGTCG
CCCGTGGAATCAGTGCCAGAACTCTGTGCAAGGGAAGCTCCTCATCGTGGATGAACCAGGCTATGTTTGCGAGAGGAGGG
ATTTGCTGGTGCAGGGCTGTAACGTCCACAGCCCTAGTGTGAAGCAGTGCTGCTGTGACGGCTGCTGGCCA

Alignment

ORF - retro_ptro_2798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.04 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WVLALVFGLSLVYFLSSTFKQEER-AVRDRNLLQVHDHNQPIPWKVQFNLGNSSRPSNQCRNSIQGKHLI
          W.........L...LSSTF.QEER..VR.R.LLQV.DH.QP.P.KVQ.NLG.SSRP.NQC.NS.QGK.LI
Retrocopy WARGALAQAILIHVLSSTFRQEER<GVRHRTLLQVQDHDQPSPCKVQVNLGSSSRPWNQCQNSVQGKLLI

Parental  TDELGYVCERKDLLVNGCCNVNVPSTKQYCCDGCWP
          .DE.GYVCER.DLLV.G.CNV..PS.KQ.CCDGCWP
Retrocopy VDEPGYVCERRDLLVQG-CNVHSPSVKQCCCDGCWP

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
SRP007412_brain_prefrontal_cortex	0.09 RPM	41.49 RPM
SRP007412_cerebellum	0.11 RPM	30.79 RPM
SRP007412_heart	0.00 RPM	7.02 RPM
SRP007412_kidney	0.03 RPM	35.62 RPM
SRP007412_liver	0.00 RPM	15.29 RPM
SRP007412_testis	0.11 RPM	19.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2798 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2798 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2376
Callithrix jacchus	retro_cjac_1471

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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 ,