RetrogeneDB ID: retro_pabe_2095

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:4015738..4016831(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARHGAP42
• Ensembl ID: ENSPPYG00000003799
• Aliases: None
• Description: Rho GTPase activating protein 42 [Source:HGNC Symbol;Acc:26545]

Sequence

>retro_pabe_2095
AAATCTTGTATCCGACGAAAGACAGATTCAATTGACAAACAATTCTGCTTCGACATACAAGTACTTGAAAGCCATGGGAT
CATCACATTACAGGCCTTCTCAGAAGCTAATAGGAAACTCTGGCTTGAAGCCACGGATGGGAAGGAGCCGATTTATACTC
TGCCTGACATTATAAGCAAGAAAGAAGAAATGTATTTGAATGAAGCAGGGTTCAATTTTGTGAGAAAATGCATTCAAGCC
ATGGAAACAAGCGGTATCACCATTTTAGGCCTCTACTGAATAGGAGGAGTGAACTCCAAAGTTCAAAAACTTGTGAATAT
CATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGACAATAATGAGTGGGCTGAAAAACT
ACCTCAAGTGCTTTGCAGGACCACTGATGACTTACAAGTTACACAAAGATTTTTATCATTGCTGTTAAATCTGATGACCA
AAACTACAGGGTGGAGGCTGTACATGCATTGGTGCACAAATTGCCAGAGAAAAACAGAGAGATGCTGGACATCTTAATAA
AACATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATGACTGTCTCAAATCTTGGTGTCATATTTGGCCCAACT
CTAATGAGAGCACAAGAACAAACTGTGGTTGCTATGGTGAATATTAAATTTCAGAATATTGTGTTAGAAATTCTTACAGA
GCATGATCAAATGATTTTTCATACTGCTCCAGACCCAAGCATTCCTCTTCCTCAGCCTCAGTCTCGATCTGGATCCCAAA
GGACACGAGCAATCTGCCTCTCTACGGGCTCTAGGAAGCCCAGAGGGACGTGTACTCCACGCCTGGCCGAACCTGATAGT
GACTCCTATAGCAGCAGCTCAGACAGCACCCCCGTGGGGAGCATCAAGTCACTCTCTTCTCTTTCCTCGGAACAAAATAG
CACTACAAAGTCAGCTTCCTGCCACCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGCAACCCCGTCATCTTCCAATG
GACAGAAAAGCCTTGGTCTCTGGACAACCAGTCCTGAATCAAGCTCTAGAGAA

Alignment

ORF - retro_pabe_2095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 56.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEESKSFLYL
          KSCIRRKTDSIDK.FCFDI.V.E.HGIITLQAFSEANRKLWLEA.DGKEPIYTLP.IISKKEE.....YL
Retrocopy KSCIRRKTDSIDKQFCFDIQVLESHGIITLQAFSEANRKLWLEATDGKEPIYTLPDIISKKEE----MYL

Parental  NEAGFNFVRKCIQAVETRGITILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNY
          NEAGFNFVRKCIQA.ET.GITILGLY.IGGVNSKVQKL.N..FSPKSPPDIDI..ELWDNKTI.SGLKNY
Retrocopy NEAGFNFVRKCIQAMETSGITILGLY*IGGVNSKVQKLVNIIFSPKSPPDIDI--ELWDNKTIMSGLKNY

Parental  LRCLAEPLMTYKLHKD-FIIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTV
          L.C.A.PLMTYKLHKD.FIIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTV
Retrocopy LKCFAGPLMTYKLHKD>FIIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTV

Parental  SNLGVIFGPTLMRAQEETVAAMMNIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICL
          SNLGVIFGPTLMRAQE.TV.AM.NIKFQNIV.EIL.EH...IFHTAPDPSIPLPQPQSRSGS.RTRAICL
Retrocopy SNLGVIFGPTLMRAQEQTVVAMVNIKFQNIVLEILTEHDQMIFHTAPDPSIPLPQPQSRSGSQRTRAICL

Parental  STGSRKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPS
          STGSRKPRG..TP.LAEPDSDSYSSS.DSTP.GSI.SLSS.SSEQNSTTKSASC.PREKSGGIPWIATPS
Retrocopy STGSRKPRGTCTPRLAEPDSDSYSSSSDSTPVGSIKSLSSLSSEQNSTTKSASCHPREKSGGIPWIATPS

Parental  SSNGQKSLGLWTTSPESSSKE
          SSNGQKSLGLWTTSPESSS.E
Retrocopy SSNGQKSLGLWTTSPESSSRE

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	0.11 RPM	1.38 RPM
SRP007412_cerebellum	0.85 RPM	1.09 RPM
SRP007412_heart	0.00 RPM	0.99 RPM
SRP007412_kidney	0.03 RPM	5.57 RPM
SRP007412_liver	0.00 RPM	2.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2095 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2095 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005829	1 retrocopy	retro_ecab_997,
Homo sapiens	ENSG00000165895	2 retrocopies	retro_hsap_2156, retro_hsap_2318,
Gorilla gorilla	ENSGGOG00000011397	2 retrocopies	retro_ggor_1714, retro_ggor_1758,
Pongo abelii	ENSPPYG00000003799	1 retrocopy	retro_pabe_2095 ,
Pan troglodytes	ENSPTRG00000004204	4 retrocopies	retro_ptro_1641, retro_ptro_1692, retro_ptro_3083, retro_ptro_892,