RetrogeneDB ID: retro_pabe_37

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:175633185..175634064(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016051
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000029405
• Aliases: None
• Description: None

Sequence

>retro_pabe_37
ATGAGCGACTTCGGCACCAAGGAGCACGCTGCACCCTTCTCCCTGGAGTACCGAGTCTTCCTCAAAAATGAGAAAGGACA
ATATATCTCTCCACTGAATATATTTCATGATATTCCAATTTATGCAGATAAGGATGTGTTCCACATGGTAGTTGAAGTAC
CACGGTGGTCTAATGCAAAAATGGAGATTGCTACAAAGGACCCTTTAAACCCCATTAAACAAGACGTGAAAAAAAGAAAA
CTTCGCTATGTTGCGAATTTGTTCCTGTATAAAGGATATATCTGGAACTATGGTGCCATCCCTCAGACTTGGGAAGACCC
AGGGCACAATGATAAACATACTGGCTGTTGTGATTACAATGACCCAATTGATGTGTGTGAAATTGGAAGCAAGGTATGTG
CAAGAGGTGAAATAATTGGTGTGAAAGTTCTGGGCATATTGGCTATGATTGACGAAGGGGAAACCGACTGGAAAGTCATT
GCCATTAATGTGGATGATCCCGATGCGGCCAATTATAATGATATCAATGATGTCAAACGGCTGAAACCCGGCTACTTAGA
GGCTGCTGTGGACTGGTTTAGAAGGAATAAGGTTCCTGATGGAAAACCAGAAAATGAGTTTGCTTTTAATGCAGAATTTA
AAGACAAGGACTTTGCAATTGATATTATTAAAAGCACTCATGACCATTGGAAAGCATTAGGGACTAAGAAAACGAATAGA
AAAGGAATCAGTTGCATGAACACAATTGTGTCTGAGAGCCCGTTCAAGTGTGATCCCGATGCTGCCAGAGCCATTGTGGA
TGCTTTGCCACCACCCTGTGAATCTGCCTGCACAGTACCAACAGACGTGGACAAGTGGTTCCATCACCAGAAAAACTAA

Alignment

ORF - retro_pabe_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCG
          MVVEVPRWSNAKMEIATKDPLNPIKQDVKK.KLRYVANLF.YKGYIWNYGAIPQTWEDPGHNDKHTGCC.
Retrocopy MVVEVPRWSNAKMEIATKDPLNPIKQDVKKRKLRYVANLFLYKGYIWNYGAIPQTWEDPGHNDKHTGCCD

Parental  DNDPIDVCEIGSKVCARGEIIGVKVLGILAMIDEGETDWKVIAINMDDPDAANYNDINDVKRLKPGYLEA
          .NDPIDVCEIGSKVCARGEIIGVKVLGILAMIDEGETDWKVIAIN.DDPDAANYNDINDVKRLKPGYLEA
Retrocopy YNDPIDVCEIGSKVCARGEIIGVKVLGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEA

Parental  TVDWFRRYKVPDGKPENEFAFNAEFKDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTVSESPFKCD
          .VDWFRR.KVPDGKPENEFAFNAEFKDKDFAIDIIKSTHDHWKAL.TKKTN.KGISCMNT.VSESPFKCD
Retrocopy AVDWFRRNKVPDGKPENEFAFNAEFKDKDFAIDIIKSTHDHWKALGTKKTNRKGISCMNTIVSESPFKCD

Parental  PDAARAIVDALPPPCESACTVPTDVDKWFHHQKN
          PDAARAIVDALPPPCESACTVPTDVDKWFHHQKN
Retrocopy PDAARAIVDALPPPCESACTVPTDVDKWFHHQKN

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	1.22 RPM	51.14 RPM
SRP007412_cerebellum	1.34 RPM	79.28 RPM
SRP007412_heart	0.54 RPM	30.80 RPM
SRP007412_kidney	0.60 RPM	25.49 RPM
SRP007412_liver	0.86 RPM	57.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_37 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_37 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040,
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Dasypus novemcinctus	ENSDNOG00000014861	1 retrocopy	retro_dnov_1310,
Equus caballus	ENSECAG00000018686	1 retrocopy	retro_ecab_691,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37 ,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,