RetrogeneDB ID: retro_pabe_839

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:49064022..49064443(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSPPYG00000004375
• Aliases: None
• Description: FGFR1 oncogene partner 2 [Source:HGNC Symbol;Acc:23098]

Sequence

>retro_pabe_839
TCTTTAGAAATGAGTTGCCCAATTGAGAAGGCACTTGCTGATGCTAAAAGTCTTGTTGAAAGATTAAGAGATCAAGATGA
TGCAGCAGAATCTCTGATTGAGCAAACCACAGCTCTCAACAAGCGAGTCGAAGCCATGAAGCAGTATCAGAAAGAAATTC
AAGAACTTAATGAAGTCGCAAGAACATCGGCCACGGTCCACATTAGTTATGGGAATCCAGCAAGAAAACAGACAAATCAG
AGAATTGCAACAAGAAAGAAAAGAATTGCGTACATCTCTGGAAGAACATCAGTCGGCCTTGGAACTTACGATGAGCAAGT
ATCGAGAACAAATGGTTAGATTGCTAATGGCTAGCAAAAAAGATGATCCGGGAATAATAATGGAAGTTAACAAGAGCAGC
ACTCCAAGGATACAAGCACAT

Alignment

ORF - retro_pabe_839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.82 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLEMSCTIEKALADAKALVERLRDHDDAAESLIEQTTALNKRVEAMKQYQEEIQELNEVAR-HRPRSTLV
          SLEMSC.IEKALADAK.LVERLRD.DDAAESLIEQTTALNKRVEAMKQYQ.EIQELNEVAR.HRPRSTLV
Retrocopy SLEMSCPIEKALADAKSLVERLRDQDDAAESLIEQTTALNKRVEAMKQYQKEIQELNEVAR>HRPRSTLV

Parental  MGIQQENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSKIDMV
          MGIQQENRQIRELQQE.KELRTSLEEHQSALEL.MSKYREQM.RLLMASKKDDPGIIM............
Retrocopy MGIQQENRQIRELQQERKELRTSLEEHQSALELTMSKYREQMVRLLMASKKDDPGIIMEVNKSSTPRIQA

Parental  H
          H
Retrocopy H

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	0.83 RPM	23.44 RPM
SRP007412_cerebellum	0.36 RPM	20.67 RPM
SRP007412_heart	0.21 RPM	9.96 RPM
SRP007412_kidney	0.40 RPM	11.04 RPM
SRP007412_liver	0.12 RPM	8.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_839 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_839 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_994
Pan troglodytes	retro_ptro_756

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839 ,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,