RetrogeneDB ID: retro_pabe_2541

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:103295459..103295960(-)
• Located in intron of: ENSPPYG00000014945

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABT1
• Ensembl ID: ENSPPYG00000016335
• Aliases: None
• Description: activator of basal transcription 1 [Source:RefSeq peptide;Acc:NP_001125836]

Sequence

>retro_pabe_2541
GAGGCAGAGGAATTGGAGAAGGCCGCAACAGAGCAAAGGCGCTGGAAGGGACAGACCAGACACTAGATGTGGAGGAGGAG
CAGGAGGAATCCAAAGCAGCAGCCTGTGCAGCAAGAAGCGGGTAGTGCCAGGTATCGTGTAACTGGGCCATATCCCACCA
CACTTCCAGCCCCTACACGTCCGCAACCTTCTCAGTGCCTGAGGTGAGGTCAGACGCGTTCTTTCAGGCTGAGGACAGGT
TTGTGAGACACAAAAAGAAGGCAGCAGCAGCCGTGGGAGGGAAAAAAGCAGTCCCACAGCAAGGACTACACCGAGGGATG
GGTGGAGTTCCGTGACAAGCGCATAGCCAAGAGCATGGCAGCCAGTCTACACAACATGCCTATGGGTGCCCACAGGTGCA
GCCCCTTCCGTTATGACCTATGGAATCTCAAGTACTTGCACCGTTTCACCTGGTCCCACCACAGCGAGCACCTTGCCTTT
GAGCGCCAGGTGCGCACACAG

Alignment

ORF - retro_pabe_2541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.27 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EAEESEKAATEQ-EPLKGTEQTLDAEEEQEESEDAACG-SKKRVVPGIVYLGHIPPRFRPLHVRNLLSAY
          EAEE.EKAATEQ...L.GT.QTLD.EEEQEES..AAC..SKKRVVPGIV.LGHIPP.F.PLHVRNLLSA.
Retrocopy EAEELEKAATEQ<KALEGTDQTLDVEEEQEESKAAACA<SKKRVVPGIV*LGHIPPHFQPLHVRNLLSA*

Parental  GEVGRVF-FQAEDRFVRRKKKAAAAAGGKKRSYSKDYTEGWVEFRDKRIAKRVAASLHNTPMGARRRSPF
          GEV.RV..F.........K........GKK.S.SKDYTEGWVEFRDKRIAK..AASLHN.PMGA.R.SPF
Retrocopy GEVRRVL<FRLRTGL*DTKRRQQQPWEGKKQSHSKDYTEGWVEFRDKRIAKSMAASLHNMPMGAHRCSPF

Parental  RYDLWNLKYLHRFTWSHLSEHLAFERQVRRQ
          RYDLWNLKYLHRFTWSH.SEHLAFERQVR.Q
Retrocopy RYDLWNLKYLHRFTWSHHSEHLAFERQVRTQ

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	6.52 RPM
SRP007412_cerebellum	0.00 RPM	8.39 RPM
SRP007412_heart	0.06 RPM	4.09 RPM
SRP007412_kidney	0.03 RPM	6.53 RPM
SRP007412_liver	0.00 RPM	8.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2541 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2541 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3066
Gorilla gorilla	retro_ggor_2106
Macaca mulatta	retro_mmul_1959

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005188	1 retrocopy	retro_chof_1748,
Cavia porcellus	ENSCPOG00000008937	1 retrocopy	retro_cpor_1386,
Gorilla gorilla	ENSGGOG00000024149	1 retrocopy	retro_ggor_2106,
Macaca mulatta	ENSMMUG00000006914	1 retrocopy	retro_mmul_1959,
Otolemur garnettii	ENSOGAG00000026316	1 retrocopy	retro_ogar_2895,
Pongo abelii	ENSPPYG00000016335	1 retrocopy	retro_pabe_2541 ,
Rattus norvegicus	ENSRNOG00000017585	1 retrocopy	retro_rnor_841,
Sarcophilus harrisii	ENSSHAG00000003493	1 retrocopy	retro_shar_97,