RetrogeneDB ID: retro_ptro_971

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:57852371..57852866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM98
• Ensembl ID: ENSPTRG00000008993
• Aliases: None
• Description: None

Sequence

>retro_ptro_971
TTAGAACTGGATGATGTTGTTATCACCAACCCCCGCATTGAGGCCATTCTGGAGAACAAAGACTGGATCGAAGATGCCTC
GGGTCTCATGTCCCACTGCATGGCCATCTTGAAGATTTGTCACACTCTGACAGAGAAGCTTGTTGCCATGACAATGGGCT
CTGGGGCCAAGATGAAGACTTCAGCCATTGTCAGCGACATCATTGTGGTGGCCAAGTGGAACAGCCCCAGGGTAGATGAT
GTTGTGAAGTCGATGTACCCGCCGTTGGACCCCAAGCTCCTGGACACAGGGACGACTACCCTGCTCCTGTCTGTCAGTCG
CCTGGTGCTGGTGACAAGGAATGCCTGCCATCTGACGGGGGGCCTGGAGTGGATTGACCAGTCACTATCAGCTGCTGAGG
AGCATTTGGAAGTCCTTCGAGAAGCAGCCCTAGCTTTTGAGCCAGATAAAGGCCTCCCAGGCCCTGAAGGCTTCCTGCAG
GAGCAGTCTGCAATT

Alignment

ORF - retro_ptro_971 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.73 %
• Parental protein coverage: 73.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LELDDVVITNPHIEAILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVSDIIVV
          LELDDVVITNP.IEAILEN.DWIEDASGLMSHC.AILKICHTLTEKLVAMTMGSGAKMKTSA.VSDIIVV
Retrocopy LELDDVVITNPRIEAILENKDWIEDASGLMSHCMAILKICHTLTEKLVAMTMGSGAKMKTSAIVSDIIVV

Parental  AKRISPRVDDVVKSMYPPLDPKLLDARTTALLLSVSHLVLVTRNACHLTGGLDWIDQSLSAAEEHLEVLR
          AK..SPRVDDVVKSMYPPLDPKLLD..TT.LLLSVS.LVLVTRNACHLTGGL.WIDQSLSAAEEHLEVLR
Retrocopy AKWNSPRVDDVVKSMYPPLDPKLLDTGTTTLLLSVSRLVLVTRNACHLTGGLEWIDQSLSAAEEHLEVLR

Parental  EAALASEPDKGLPGPEGFLQEQSAI
          EAALA.EPDKGLPGPEGFLQEQSAI
Retrocopy EAALAFEPDKGLPGPEGFLQEQSAI

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	0.04 RPM	24.15 RPM
SRP007412_cerebellum	0.04 RPM	20.43 RPM
SRP007412_heart	0.00 RPM	5.04 RPM
SRP007412_kidney	0.00 RPM	42.44 RPM
SRP007412_liver	0.00 RPM	15.91 RPM
SRP007412_testis	1.16 RPM	3.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_971 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_971 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1421
Gorilla gorilla	retro_ggor_1098
Pongo abelii	retro_pabe_1175
Macaca mulatta	retro_mmul_2256

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014550	1 retrocopy	retro_cjac_2447,
Homo sapiens	ENSG00000006042	2 retrocopies	retro_hsap_1421, retro_hsap_3605,
Gorilla gorilla	ENSGGOG00000013333	2 retrocopies	retro_ggor_1098, retro_ggor_2432,
Myotis lucifugus	ENSMLUG00000001191	1 retrocopy	retro_mluc_130,
Macaca mulatta	ENSMMUG00000022356	2 retrocopies	retro_mmul_1835, retro_mmul_2256,
Nomascus leucogenys	ENSNLEG00000006038	3 retrocopies	retro_nleu_1233, retro_nleu_1840, retro_nleu_2635,
Pongo abelii	ENSPPYG00000008166	2 retrocopies	retro_pabe_1175, retro_pabe_2961,
Pan troglodytes	ENSPTRG00000008993	3 retrocopies	retro_ptro_2436, retro_ptro_2990, retro_ptro_971 ,