RetrogeneDB ID: retro_ptro_144

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:47119901..47120513(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHSA2
• Ensembl ID: ENSPTRG00000023268
• Aliases: None
• Description: AHA1, activator of heat shock 90kDa protein ATPase homolog 2 (yeast) [Source:HGNC Symbol;Acc:20437]

Sequence

>retro_ptro_144
ACTGAGTGGGATGCCACCAGCTGGTCCAAAGAGAAGCTCCAGGAGCTCCTGGTGGTCATCGTTGTGGAGGATGAGGCTGG
CCACTGAGAGATCAGCGAGCTAAAGCAGGTGGAAGGTAAGGCTTCTTGCAGCATCCACAAAGGAAAGGTGATTTTCTTGT
ATGAGTGAAACATCAAACTAGGCTGGAAAGGTATCATTAAAGAATCTGACGTGAACCACAAGGGATTGATTGAGATACCC
AATCTTTCTGAAGAAAATGAAGTAGATGACACCGAGGTGAATGTGAGTAAAAAGAAAGGAGATGGGGATATACCGAATGA
TCTTATGAAAACTGCAGGCACTGCCAAGGTCAGGGAGGAGGTCCTTGGAGATTATCTGAAGACACTCAAGACAGAATTTA
CAATGGGAATGGTTTTACCAGTGAAAACTATGGCAACCTAGGAATTGACTGTTAAAAGAAAATGGAGCGAGAATATCTTG
CAGGTTCGGGCCTCATCTCCAGTGGCACTGGGTGTAAGAATTCCCGCTATGGCTCTTCCCATCAGGGCACAGTTTGACGT
AACTGTAGAACAGCTGTACAGCATCTTCACTATGAAGAATTTGGTGCAAAAA

Alignment

ORF - retro_ptro_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 68.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TERDATSWSKGKFQELLVGIAVENDAGRGEINELKQVEGEASCSSRKGKLIFFYQWNIKLGWKGIVKESG
          TE.DATSWSK.K.QELLV.I.VE..AG..EI.ELKQVEG.ASCS..KGK.IF.Y..NIKLGWKGI.KES.
Retrocopy TEWDATSWSKEKLQELLVVIVVEDEAGH*EISELKQVEGKASCSIHKGKVIFLYE*NIKLGWKGIIKESD

Parental  VKHKGLIEIPNLSEENEVDDTEVS-SKKKGDGVVLKDLMKTAGTAKVR-EALGDYLKALKTEFTTGMILP
          V.HKGLIEIPNLSEENEVDDTEV..SKKKGDG....DLMKTAGTAKVR.E.LGDYLK.LKTEFT.GM.LP
Retrocopy VNHKGLIEIPNLSEENEVDDTEVNVSKKKGDGDIPNDLMKTAGTAKVREEVLGDYLKTLKTEFTMGMVLP

Parental  TKAMATQELTVKRKLSGNTLQVQASSPVALGVRIPTVALHMMELFDTTVEQLYSIFTVKDLTKK
          .K.MAT.ELTVKRK.S.N.LQV.ASSPVALGVRIP..AL.....FD.TVEQLYSIFT.K.L..K
Retrocopy VKTMAT*ELTVKRKWSENILQVRASSPVALGVRIPAMALPIRAQFDVTVEQLYSIFTMKNLVQK

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	0.00 RPM	11.65 RPM
SRP007412_cerebellum	0.00 RPM	20.76 RPM
SRP007412_heart	0.00 RPM	8.13 RPM
SRP007412_kidney	0.00 RPM	20.06 RPM
SRP007412_liver	0.00 RPM	10.18 RPM
SRP007412_testis	0.00 RPM	39.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_144 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_144 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_237
Pongo abelii	retro_pabe_471

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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,