RetrogeneDB ID: retro_pabe_2356

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:142112071..142112733(-)
• Located in intron of: ENSPPYG00000014158

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSPPYG00000006464
• Aliases: None
• Description: DTW domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RCQ0]

Sequence

>retro_pabe_2356
ATGTCTCTCAATCCACCTATATTTCTCAAACGAAGTGAAGAAAATAATTCAAAATTTGTGGAAACAAAACAGTCACAAAC
TACTTCCATAGCTTCAGAAGATCCCCTTCAAAACTTATGTTTAGCATCTCAAGAAGTTCTTCAAAAAGCTCAGCAAAGTG
GGAGATCATAATGTCTCAAATGTGGTAGTTCCAGAATGTTCTACTGCTATACATGTTACGTTCCAGTTGAAAATGTACCT
ATTGAACAGATTCCCTTGTGAAGCTTCCATTGAAGATTGACATCATTAAACATCCAAATGAAACAGATGGTAAAAGTACT
GCTATACATGCAAAATTCTTAGCACCTGAATTTGTAAACATTTACACGTATTCTTGTATTCCAGAATATGAAGAAAAGGA
CCATGAAGTTGCACTTGTTTTTCCTCAGTCTATCTCAATAAAAGATATTTGTTTTCATCTGCAAAAAAGGATTCAAAATA
ATGTTAGCAGCAAAAATGATGACCCTGACAAGCCATCTTTTAAACGCAAAAGAACTGAAGAACAAGAGTTCTGTGATTTG
AATGACAGCAAGTGCAAAGGCACAACACTGAAAAAAATTATATTTATAGATAGCACCTGGAACCAAACAAACAAAATATT
CACTGATGAGCGACTTCAAGGT

Alignment

ORF - retro_pabe_2356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 73.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLNPPIFLKRSEENNSKFVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRSKCLKCGGSRMFYCY
          MSLNPPIFLKRSEENNSKFVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRS.CLKCG.SRMFYCY
Retrocopy MSLNPPIFLKRSEENNSKFVETKQSQTTSIASEDPLQNLCLASQEVLQKAQQSGRS*CLKCGSSRMFYCY

Parental  TCYVPVENVPIEQIP-LVKLPLKIDIIKHPNETDGKSTAIHAKLLAPEFVNIYTYPCIPEYEEKDHEVAL
          TCYVPVENVPIEQIP.LVKLPLKIDIIKHPNETDGKSTAIHAK.LAPEFVNIYTY.CIPEYEEKDHEVAL
Retrocopy TCYVPVENVPIEQIP<LVKLPLKIDIIKHPNETDGKSTAIHAKFLAPEFVNIYTYSCIPEYEEKDHEVAL

Parental  VFPGPQSISIKDISFHLQKRIQNNVRGKNDDPDKPSFKRKRAEEQEFCDLNDSKCKGTTLKKIIFIDSTW
          VF..PQSISIKDI.FHLQKRIQNNV..KNDDPDKPSFKRKR.EEQEFCDLNDSKCKGTTLKKIIFIDSTW
Retrocopy VF--PQSISIKDICFHLQKRIQNNVSSKNDDPDKPSFKRKRTEEQEFCDLNDSKCKGTTLKKIIFIDSTW

Parental  NQTNKIFTDERLQG
          NQTNKIFTDERLQG
Retrocopy NQTNKIFTDERLQG

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	4.81 RPM
SRP007412_cerebellum	0.00 RPM	4.99 RPM
SRP007412_heart	0.00 RPM	2.14 RPM
SRP007412_kidney	0.00 RPM	3.15 RPM
SRP007412_liver	0.03 RPM	1.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2356 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2356 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014926	1 retrocopy	retro_cfam_2081,
Cavia porcellus	ENSCPOG00000003461	2 retrocopies	retro_cpor_1476, retro_cpor_250,
Homo sapiens	ENSG00000104047	1 retrocopy	retro_hsap_2846,
Gorilla gorilla	ENSGGOG00000027921	1 retrocopy	retro_ggor_1973,
Nomascus leucogenys	ENSNLEG00000006167	1 retrocopy	retro_nleu_1598,
Otolemur garnettii	ENSOGAG00000013291	1 retrocopy	retro_ogar_499,
Ochotona princeps	ENSOPRG00000002951	2 retrocopies	retro_opri_136, retro_opri_949,
Pongo abelii	ENSPPYG00000006464	2 retrocopies	retro_pabe_2355, retro_pabe_2356 ,
Pan troglodytes	ENSPTRG00000007058	1 retrocopy	retro_ptro_1928,
Vicugna pacos	ENSVPAG00000008358	2 retrocopies	retro_vpac_509, retro_vpac_530,