RetrogeneDB ID: retro_pabe_471

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:183139757..183140508(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHSA2
• Ensembl ID: ENSPPYG00000012385
• Aliases: None
• Description: AHA1, activator of heat shock 90kDa protein ATPase homolog 2 (yeast) [Source:HGNC Symbol;Acc:20437]

Sequence

>retro_pabe_471
ACTGAGTGGGATGCCACCAGCTGGTCCAAAGAGAAGCTCCAGGAGCTCCTGGTTGTCATCGTTGTGGAAGATGAAGCTGG
CCACTGAGAGATCAGTGAGCTGAAGCAGGTGGAAGGTAAGGCTTCTTGCAGCATCCGCAAAGGAAAGGTGATTTTCTTGT
ATGAGTGGAACATCAAACTGGGCTGGAAAGGTATCATTAAAAAATCTGACGTGAACCACAAGGGGTTGATTGAAATATCC
AGTCTTTCTGAAGAAAATGAAGTATGACACCGAGGCGAACGTGAGTAAAAAGAAAGGAGATGGGGATATACTGAATGATC
TTATGAAAACTGCAGGCACTGCCAAGGTCAGGGAGGAGGTCCTTGGAGATTACCTGAAGGCACTCAAGACAGAATTTACA
ATGGGAATGGTTTTACCAGTGAAAAACATGGCAACCTAGGAATTGACTGTTAAAAGAAAATGGAGTGAGAATATCTTGCA
GGTTTGGGCCTCATCTCCAGTGGCACTGGGTATGAGAATTCCCACTATGGCTCTTCCCATGAGGGAACAGTTTGACACAA
CTGTAGAACAGCTGTACAGCATCTTCACTGTGAAGGATTTGGTGCAAAAATTTTCTAAATCTCCTGCTGTATTAGAAGCT
GAAAAGGGAGGGAAATTCCAAATGTTTGATGGGAACATCACTGATGAATATATAGAATTGTTAACAAATAAAAAAGTCAT
AATGAAATGGAGATGTAGGAACTGGCCAGAA

Alignment

ORF - retro_pabe_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.59 %
• Parental protein coverage: 75.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TERDATSWSKGKFRELLVGIVVENDVGRGEISELKQVEGEASCSSRKGKLIFFYEWNIKLDWKGIVKESG
          TE.DATSWSK.K..ELLV.IVVE...G..EISELKQVEG.ASCS.RKGK.IF.YEWNIKL.WKGI.K.S.
Retrocopy TEWDATSWSKEKLQELLVVIVVEDEAGH*EISELKQVEGKASCSIRKGKVIFLYEWNIKLGWKGIIKKSD

Parental  VKH-KGLIEIPSLSEENEVSDTEVNVSKKKGDGDILKDLTKTAGTAKVRE-ALGDYLKALKTEFTTGMIL
          V.H..G....P.........DTE.NVSKKKGDGDIL.DL.KTAGTAKVRE..LGDYLKALKTEFT.GM.L
Retrocopy VNH>RG*LKYPVFLKKMKY-DTEANVSKKKGDGDILNDLMKTAGTAKVREEVLGDYLKALKTEFTMGMVL

Parental  PTKAMATQELTVKRKLSENTLQ--ASSPVALGVRIPTVALHMMELFDTTVEQLYSIFTVKDLVQKFSKST
          P.K.MAT.ELTVKRK.SEN.LQ..ASSPVALG.RIPT.AL.M.E.FDTTVEQLYSIFTVKDLVQKFSKS.
Retrocopy PVKNMAT*ELTVKRKWSENILQVWASSPVALGMRIPTMALPMREQFDTTVEQLYSIFTVKDLVQKFSKSP

Parental  AVLEAEKGGKFQMFDGNITGEYLELLTS-KIIMKWRCRNWPE
          AVLEAEKGGKFQMFDGNIT.EY.ELLT..K.IMKWRCRNWPE
Retrocopy AVLEAEKGGKFQMFDGNITDEYIELLTNKKVIMKWRCRNWPE

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	0.06 RPM	25.93 RPM
SRP007412_cerebellum	0.49 RPM	75.03 RPM
SRP007412_heart	0.03 RPM	10.69 RPM
SRP007412_kidney	0.00 RPM	27.48 RPM
SRP007412_liver	0.00 RPM	15.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_471 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_471 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_144
Gorilla gorilla	retro_ggor_237

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034768	1 retrocopy	retro_cjac_2904,
Equus caballus	ENSECAG00000005107	1 retrocopy	retro_ecab_217,
Gorilla gorilla	ENSGGOG00000014565	1 retrocopy	retro_ggor_237,
Pongo abelii	ENSPPYG00000012385	1 retrocopy	retro_pabe_471 ,
Pan troglodytes	ENSPTRG00000023268	1 retrocopy	retro_ptro_144,
Tursiops truncatus	ENSTTRG00000013366	1 retrocopy	retro_ttru_1173,