RetrogeneDB ID: retro_ptro_2278

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:82670511..82671141(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSPTRG00000001864
• Aliases: None
• Description: None

Sequence

>retro_ptro_2278
ATGGCCCGGGGGCCCGGCCAGCTAGGCAGGCCTCGCCCCGATACGGTCGCCATGCCCAAGAGAGGAAAGCGACTCAAGTT
CTGGGCCCACGACGCCTGCTCTGGACAAGTGATTGAGGTGGATGACGCCAACTCGGATCCAGCGGTCGTGAGGTCTGGAT
GAGTCAAGAGAGCCTTAGCCAACACTGTTCAGCAGGAAGTAAAATCTCTTTGTGGCTTGGAAGCCTCTCAGGTTCCTGCA
GAGGAAGCTCTTTCTGGGGCTGGTGAGCCCTGTGACATCATCGACAGCGGTGATGAGACGGATGCCCAGGAGGAAAGCAT
CCGTGAGAGAACTGTCTCCAGAAAAAAGAAAAGCGAGAGGCACAAAGAAGAACTGAACGGGGCTGGAGGAGAAGAGTATC
CCATGGATATTTGGCTATTGCTGGCCTCCTATATCCGTCCTGAGGACATTGTGAATTTTCCCCTGATTTGTAAGAATGCT
TGGACTGTCACTTGCACTGCTGCCTTTTGGACCAGGTTGTACCGAAGGCACTACACGCTGGATGCTTCCCTGCCTTTGCG
TCTGCGACCAGAGTCAATGGAGAAGCTGCGCTGTCTCGGGGCTTGTGTGATCCGATCTCTGTACCATATA

Alignment

ORF - retro_ptro_2278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.95 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARGPGPLGRPRPDTVAMPKRGKRLKFRAHDACSGRVTVADYANSDPAVVRSGRVKKAVANAVQQEVKSL
          MARGPG.LGRPRPDTVAMPKRGKRLKF.AHDACSG.V...D.ANSDPAVVRSG.VK.A.AN.VQQEVKSL
Retrocopy MARGPGQLGRPRPDTVAMPKRGKRLKFWAHDACSGQVIEVDDANSDPAVVRSG*VKRALANTVQQEVKSL

Parental  CGLEASQVPAEEALSGAGEPCDIIDSSDEMDAQEESIHERTVSRKKKSKRHKEELDGAGGEEYPMDIWLL
          CGLEASQVPAEEALSGAGEPCDIIDS.DE.DAQEESI.ERTVSRKKKS.RHKEEL.GAGGEEYPMDIWLL
Retrocopy CGLEASQVPAEEALSGAGEPCDIIDSGDETDAQEESIRERTVSRKKKSERHKEELNGAGGEEYPMDIWLL

Parental  LASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSLYHM
          LASYIRPEDIVNF.LICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCL.ACVIRSLYH.
Retrocopy LASYIRPEDIVNFPLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLGACVIRSLYHI

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	0.11 RPM	68.05 RPM
SRP007412_cerebellum	0.07 RPM	51.80 RPM
SRP007412_heart	0.00 RPM	14.89 RPM
SRP007412_kidney	0.03 RPM	44.98 RPM
SRP007412_liver	0.00 RPM	27.99 RPM
SRP007412_testis	0.00 RPM	92.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2278 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2278 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3157
Gorilla gorilla	retro_ggor_1358
Pongo abelii	retro_pabe_2627

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278 ,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,