RetrogeneDB ID: retro_pabe_1277

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:23597428..23597978(-)
• Located in intron of: ENSPPYG00000006277

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP3
• Ensembl ID: ENSPPYG00000008353
• Aliases: DUSP3, VHR
• Description: Dual specificity protein phosphatase 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5RD73]

Sequence

>retro_pabe_1277
ATGACAGGCCCTTTCAAATGCTCCATGGAAGTTCTCAATGACCTGCTCTCAGATAGCAGTGGCTGCTACAGCCTCCCAAG
CCAGCCCTGCAATGAGGTCACCCTGAGGATTTACATGGGCAACACATCTGTGGCTCAGGATATCCCCAAGCTTCAGAAAC
TGGTCAGGATTCATGTCCTGAATGCCACTGAGGGCAGGTCTTTCATGCACATAAACAATGCCAACTTCTCCAAGGACTCT
GGCATCACCTACCTGGGCATCAAGACCATTGAAGTGCAGGAGTTCAACCTCAGCACCTATTTTGAAAGGGCTACAGACTT
CACTGACCAGGCCTTGGCTCAAAAGAATGGCCAGGTGCTCGTCCAGTGCTGGGAAGGTTACAGCCATCTCCAGCTCTAGT
TATCATGTACCTCACGATTGTAAGAAGTTGGACATCAAGTCCATCCTGAGTATCATGAGGCAGAACTGTGAGATCAGCCC
CAATGATGGGTTCCTGGCTCAGCTTTGCCATCTCAATGACAAACTAGCCAAGGAGGGGAAGGTGAAACCC

Alignment

ORF - retro_pabe_1277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGSFELSVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMH
          M.G.F..S...LNDLLSD.SGCYSLPSQPCNEVT.RIY.GN.SVAQDIPKLQKL...HVLNA.EGRSFMH
Retrocopy MTGPFKCSMEVLNDLLSDSSGCYSLPSQPCNEVTLRIYMGNTSVAQDIPKLQKLVRIHVLNATEGRSFMH

Parental  VNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSR-SPTLVIAYL
          .N.NANF.KDSGITYLGIK....QEFNLS.YFERA.DF.DQALAQKNG.VLV.C.EGYS..SP.LVI.YL
Retrocopy IN-NANFSKDSGITYLGIKTIEVQEFNLSTYFERATDFTDQALAQKNGQVLVQCWEGYSH<SPALVIMYL

Parental  MM-RQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP
          .....K.D.KS.LSI.RQN.EI.PNDGFLAQLC.LND.LAKEGK.KP
Retrocopy TI<CKKLDIKSILSIMRQNCEISPNDGFLAQLCHLNDKLAKEGKVKP

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	170.35 RPM
SRP007412_cerebellum	0.00 RPM	103.12 RPM
SRP007412_heart	0.00 RPM	152.84 RPM
SRP007412_kidney	0.00 RPM	120.65 RPM
SRP007412_liver	0.00 RPM	82.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1277 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1277 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1541
Gorilla gorilla	retro_ggor_1174
Macaca mulatta	retro_mmul_2205

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108861	1 retrocopy	retro_hsap_1541,
Gorilla gorilla	ENSGGOG00000023681	1 retrocopy	retro_ggor_1174,
Macaca mulatta	ENSMMUG00000002351	1 retrocopy	retro_mmul_2205,
Nomascus leucogenys	ENSNLEG00000005702	1 retrocopy	retro_nleu_2391,
Pongo abelii	ENSPPYG00000008353	1 retrocopy	retro_pabe_1277 ,