RetrogeneDB ID: retro_pabe_1812

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:20920358..20920748(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AES
• Ensembl ID: ENSPPYG00000009364
• Aliases: None
• Description: amino-terminal enhancer of split [Source:HGNC Symbol;Acc:307]

Sequence

>retro_pabe_1812
GGATTAAACATTGAAATGCATAAACGGACTCTAATCGCCAAGAGATTGAATACGATTTGTGCAAAAGTCATCCCATTTCT
GGGATGGGAACATCAACGACAGATGGCCCAGGCTGTCGAACGTGCCAAACAGGTTACCATGGCACCTGTTTGAATGCCAT
CATCGGGCAGCAACAGCTGCAAACTCAGCATCTTTCATGGCCACAGACCCCCGTTCCCCTTACTCCTCACCCTTGGAGAC
TTCAGCCTCCTGGAATCTCGCTCCTCGGGGGCCGTGCTGGCCTTCTTGCGCTGCCTAGTGCTCTGAGTGGGCAGTCTTAT
TTGGCAATACAAGGTGACAAAGCACCATGATGCAGAGCACCACAGAGGTGAGAGGCCGGGCAAGCCAGAT

Alignment

ORF - retro_pabe_1812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.38 %
• Parental protein coverage: 75.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLNIEMHKQAEIVKRLNGICAQVLPYLSQEHQQQVLGAIERAKQVT-APE-LNSII-RQQLQAHQLSQLQ
          GLNIEMHK...I.KRLN.ICA.V.P.L..EHQ.Q...A.ERAKQVT.AP..LN.II..QQLQ...LS..Q
Retrocopy GLNIEMHKRTLIAKRLNTICAKVIPFLGWEHQRQMAQAVERAKQVTMAPV<LNAIIGQQQLQTQHLSWPQ

Parental  ALALPLTPLPVGLQPPSLPAVSAGTGLLSL-SALGSQAHLSKEDKNG-HDGDTHQEDDGEKSD
          ....PLTP.P..LQPP.........GLL.L.SAL..Q..L........HD...H......K.D
Retrocopy T-PVPLTPHPWRLQPPGISLLGGRAGLLALPSALSGQSYLAIQGDKA>HDAEHHRGERPGKPD

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	100.63 RPM
SRP007412_cerebellum	0.00 RPM	56.18 RPM
SRP007412_heart	0.09 RPM	40.88 RPM
SRP007412_kidney	0.00 RPM	56.02 RPM
SRP007412_liver	0.00 RPM	47.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1812 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1812 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031363	1 retrocopy	retro_btau_342,
Otolemur garnettii	ENSOGAG00000016151	2 retrocopies	retro_ogar_1674, retro_ogar_2148,
Pongo abelii	ENSPPYG00000009364	2 retrocopies	retro_pabe_1812 , retro_pabe_2155,