RetrogeneDB ID: retro_pabe_2209

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:32542577..32543003(+)
• Located in intron of: ENSPPYG00000013598

Retrocopy information

• Ensembl ID: ENSPPYG00000013599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSPPYG00000005830
• Aliases: None
• Description: Glia maturation factor beta [Source:UniProtKB/Swiss-Prot;Acc:Q5R6P6]

Sequence

>retro_pabe_2209
ATGAGTGAGTCTTTGGTGGTTTTGATGTTGCTGAAGATTTAGTGGAAAAGCTGAGAAAGTTTCGTTTTCACAAAGAAACG
AACAATGCTGCTATTATAATGAAGACTGACAAGGATAAACACCTGGTGGTGCTGGATGAGGAGCTTGAGGGTATTTCTCC
AGATGAACTTAAAGATGAACTACCTGAACGACAACCTTGTTTCATTATGTATAGTTATAAATATCAACATAATGGATGGG
AGAGTTCCATATCCTCTGTGCTTTATTTTCTCCAGTCCTGTTGGATGTAAGCCTGAACAACAAATGATATATGCTGGCAG
TAAGAATAAGCTAGTCCAGACAGCTGAACTAACCAAGGTATTTGAAATAAGAAATACGGAAGACCTGACTGAAGAATGGT
TATGTGAGAAACTTGGATTTTTCCAC

Alignment

ORF - retro_pabe_2209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSESLVVC-DVAEDLVEKLRKFRFRKETNNAAIIMKIDKDKRLVVLDEELEGISPDELKDELPERQPRFI
          MSESLVV..DVAEDLVEKLRKFRF.KETNNAAIIMK.DKDK.LVVLDEELEGISPDELKDELPERQP.FI
Retrocopy MSESLVVL<DVAEDLVEKLRKFRFHKETNNAAIIMKTDKDKHLVVLDEELEGISPDELKDELPERQPCFI

Parental  VYSYKYQHD-DGRVSYPLCFIF-SPVGCKPEQQMMYAGSKNKLVQTAELTKVFEIRNTEDLTEEWLREKL
          .YSYKYQH..DGRV.YPLCFIF.SPVGCKPEQQM.YAGSKNKLVQTAELTKVFEIRNTEDLTEEWL.EKL
Retrocopy MYSYKYQHN>DGRVPYPLCFIFSSPVGCKPEQQMIYAGSKNKLVQTAELTKVFEIRNTEDLTEEWLCEKL

Parental  GFFH
          GFFH
Retrocopy GFFH

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	0.17 RPM	45.23 RPM
SRP007412_cerebellum	0.24 RPM	78.19 RPM
SRP007412_heart	0.03 RPM	12.28 RPM
SRP007412_kidney	0.00 RPM	29.24 RPM
SRP007412_liver	0.06 RPM	14.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2209 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2209 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2818
Gorilla gorilla	retro_ggor_1960
Macaca mulatta	retro_mmul_1498

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007312	1 retrocopy	retro_cjac_736,
Cavia porcellus	ENSCPOG00000004207	1 retrocopy	retro_cpor_240,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493,
Macaca mulatta	ENSMMUG00000012326	1 retrocopy	retro_mmul_1498,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849, retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209 ,