RetrogeneDB ID: retro_ptro_2263

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:50613077..50613356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL49
• Ensembl ID: ENSPTRG00000003867
• Aliases: None
• Description: None

Sequence

>retro_ptro_2263
TTTGCAGAGTGACTGTTACTCTTCACTAGGATCCCAAAGTCCCCAAGGCATGAACATTATCCCACCCCAATGGCTGGCAA
CCTCCCAGAGAAACCCCCAACCCCACCCAATCTGCCCTACTTGGTGCAGTGCCCTCAGATGCACAAAATCCTTGTCTATA
AGGACATCACACATGGCAACTTTCAGATGACTGTGACCCCAAAGGTGGAGGGGGACATCTGGGCGCTGCTGAAGGATGTG
GAGGATTTTCTGAGCCCACTGCTGGGAAAGACACCTGTT

Alignment

ORF - retro_ptro_2263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.63 %
• Parental protein coverage: 54.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FVERLLPATRIPDPPKHEHYPTP-SGWQP-PRDPP--PNLPYFVRRSRMHNIPVYKDITHSNRQMTVIRK
          F.E.LL..TRIP..P.HEHYPTP..GWQP.P..PP..PNLPY.V....MH.I.VYKDITH.N.QMTV..K
Retrocopy FAE*LLLFTRIPKSPRHEHYPTP<NGWQP>PEKPPTPPNLPYLVQCPQMHKILVYKDITHGNFQMTVTPK

Parental  VEGDIWALQKDVEDFLSPLLGKTPV
          VEGDIWAL.KDVEDFLSPLLGKTPV
Retrocopy VEGDIWALLKDVEDFLSPLLGKTPV

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	0.00 RPM	34.32 RPM
SRP007412_cerebellum	0.00 RPM	28.71 RPM
SRP007412_heart	0.00 RPM	22.03 RPM
SRP007412_kidney	0.00 RPM	59.05 RPM
SRP007412_liver	0.00 RPM	27.07 RPM
SRP007412_testis	0.00 RPM	9.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2263 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2263 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3180

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012855	1 retrocopy	retro_chof_1006,
Dasypus novemcinctus	ENSDNOG00000004494	6 retrocopies	retro_dnov_1396, retro_dnov_1488, retro_dnov_1941, retro_dnov_2272, retro_dnov_2473, retro_dnov_2686,
Dipodomys ordii	ENSDORG00000003613	1 retrocopy	retro_dord_196,
Homo sapiens	ENSG00000149792	1 retrocopy	retro_hsap_3180,
Macropus eugenii	ENSMEUG00000009437	1 retrocopy	retro_meug_1151,
Microcebus murinus	ENSMICG00000016604	1 retrocopy	retro_mmur_629,
Macaca mulatta	ENSMMUG00000018778	1 retrocopy	retro_mmul_2031,
Nomascus leucogenys	ENSNLEG00000005505	1 retrocopy	retro_nleu_1659,
Oryctolagus cuniculus	ENSOCUG00000014882	1 retrocopy	retro_ocun_316,
Pan troglodytes	ENSPTRG00000003867	1 retrocopy	retro_ptro_2263 ,
Tupaia belangeri	ENSTBEG00000007929	2 retrocopies	retro_tbel_1350, retro_tbel_3334,