RetrogeneDB ID: retro_ptro_1020

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:57031269..57031830(+)
• Located in intron of: ENSPTRG00000007130

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGH
• Ensembl ID: ENSPTRG00000006466
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class H [Source:HGNC Symbol;Acc:8964]

Sequence

>retro_ptro_1020
ATGGAGGATGAGCGGAGCTTTTCGGATATCTGCGGTGGCCGCCTGGCCCTGCAGCGCCGCTACTACTCCCCTTCCTGCCG
GGAATTCTGCCTCAGCTGCCCTGGGCTCTCGCTGCGTTCGCTCACCGCTGTCACCTGCACGGTGTGGCTGGCAGCCTACG
GACTCTTCACCCTCTGCGAGAACAGCATGATCCTCTCTGCTGCCATCTTCATCACCCTCTTAGGTCTGCTTGGTTATCTC
CATTTTGTGAAGATTGATCAGGAGACTGTTAATCATTGATTCCCTTGGCATTCAGATGACTTCATCTTATGCTTTAGGCT
AAGAAAGCACTACCGTCATAGAAATGGGCAAGGTCAAGGATATTGTCATCAATGAGGCTATTTACATGCAGAAGGTGATT
TACTACCTCTGCATCTTATTGAAGGATCCAGTGGAACCACATGGGATATCCCAAGTAGTACCCGTCTTCTAGAGTGCCAA
GCCCCGGTGGACTGCTTGACTGAAGTATACAGGAGCTGCCAGGGGATCCTGGCACACCAGAAAGCCACATCAACAAGCCC
A

Alignment

ORF - retro_ptro_1020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEDERSFSDICGGRLALQRRYYSPSCREFCLSCPRLSLRSLTAVTCTVWLAAYGLFTLCENSMILSAAIF
          MEDERSFSDICGGRLALQRRYYSPSCREFCLSCP.LSLRSLTAVTCTVWLAAYGLFTLCENSMILSAAIF
Retrocopy MEDERSFSDICGGRLALQRRYYSPSCREFCLSCPGLSLRSLTAVTCTVWLAAYGLFTLCENSMILSAAIF

Parental  ITLLGLLGYLHFVKIDQET-LLIIDSLGIQMTSSYASGKESTTFIEMGKVKDIVINEAIYMQKVIYYLCI
          ITLLGLLGYLHFVKIDQET.L.I.DSLGIQMTSSYA.G.ESTT.IEMGKVKDIVINEAIYMQKVIYYLCI
Retrocopy ITLLGLLGYLHFVKIDQET>LII-DSLGIQMTSSYALG*ESTTVIEMGKVKDIVINEAIYMQKVIYYLCI

Parental  LLKDPVEPHGISQVVPVFQSAKPR-LDCLIEVYRSCQEILAHQKATSTSP
          LLKDPVEPHGISQVVPVF.SAKPR..DCL.EVYRSCQ.ILAHQKATSTSP
Retrocopy LLKDPVEPHGISQVVPVF*SAKPR<VDCLTEVYRSCQGILAHQKATSTSP

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	0.07 RPM	23.18 RPM
SRP007412_cerebellum	0.25 RPM	15.56 RPM
SRP007412_heart	0.03 RPM	7.00 RPM
SRP007412_kidney	0.24 RPM	23.85 RPM
SRP007412_liver	0.20 RPM	7.73 RPM
SRP007412_testis	0.00 RPM	16.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1020 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1020 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1020 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1506
Gorilla gorilla	retro_ggor_1155
Pongo abelii	retro_pabe_1255

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003328	1 retrocopy	retro_cpor_815,
Echinops telfairi	ENSETEG00000008623	1 retrocopy	retro_etel_844,
Homo sapiens	ENSG00000100564	1 retrocopy	retro_hsap_1506,
Gorilla gorilla	ENSGGOG00000001507	1 retrocopy	retro_ggor_1155,
Macropus eugenii	ENSMEUG00000011325	1 retrocopy	retro_meug_2130,
Myotis lucifugus	ENSMLUG00000004467	1 retrocopy	retro_mluc_910,
Nomascus leucogenys	ENSNLEG00000000739	1 retrocopy	retro_nleu_1747,
Pongo abelii	ENSPPYG00000005925	1 retrocopy	retro_pabe_1255,
Pan troglodytes	ENSPTRG00000006466	1 retrocopy	retro_ptro_1020 ,
Tarsius syrichta	ENSTSYG00000008465	1 retrocopy	retro_tsyr_1926,