RetrogeneDB ID: retro_pabe_320

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:174744633..174745701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR48
• Ensembl ID: ENSPPYG00000014001
• Aliases: None
• Description: WD repeat-containing protein 48 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAW8]

Sequence

>retro_pabe_320
ATGGCGGCCCATCACCGGCAGAAGACAGCAGGGCGGAGGAAAGTGCAGGTTTCCTATGTTATTCAAGATGAAGTGGAGAA
GTACAACCGAAATGGAGTCAATGCTCTGCAGCTGGATCCAGCACTAAATAGACTTTTCACAGCCGGTCGAGACTCTATCA
TAAGAATATGGAGTGTCAATCAGCACAAGCAAGATCCGTATATAGCATCTATGGAACACCATACTGATTGGGTAAATGAC
ATTGTACTCTGTTGTAATGGGAAAACATTAATATCTGCTTCTTCTGACACAACAGTAAAAGTATGGAATGCACACAAGGG
ATTTTTCATGTCAACATTAAGGACACATAAGGATTACGTAAAGGCCTTAGCATATGCCAAGGATAAAGAACTAGTAGCAT
CAGCTGGGTTGGACAGATAAATATTCCTTTTGGATGTGAATACTCTAACAGCATTGACTGCCTCAAATAACACTGTCACA
ACTTCTTCTTTAAGTGGAAACAAAGATTCCATTTATAGCCTGGCCATGAATCAACTGGGAACAATCATTGTATCAGGGTC
CACTGAAAAGGTGTTAAGGGTATGGGATCCAAGAACATGTGCAAAACTAATGAAGCTTAAAGGGCACATGGATAATGTGA
AGGCATTGCTATTAAACAGAGATGGCACGCAATGCCTTTCAGGCAGTTCTGATGGGACAATTCGCCTTTGGTCCCTTGGC
CAGCAGAGATATATAGCAACATACCGAGTCCATGATGAAGGTGTTTGGGCGCTGCAAGTCAATGATGCCTTCACATATGT
GTATTCTGGTGGAAGGGACAGGAAGATTTATTGTACAGACCTAAGAAACCCTGACATTCGGGTGCTAATTTGTGAAGAAA
AAGCACCAGTTCTCAAGATGGAGCTTGATAGATCAGCTGATCCTCCTCCTGCAATTTGGGTTGCAACAACTAAGTCTACA
GTAAATAAATGGACTTTGAAAGGAATTCATAATTTTAGAGCCTCTGGAGATTATGACAATGACTGTACAAATCCTATAAC
ACCTCTTTGTACACAACCTGACCAGGTT

Alignment

ORF - retro_pabe_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.47 %
• Parental protein coverage: 52.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAHHRQNTAGRRKVQVSYVIRDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS
          MAAHHRQ.TAGRRKVQVSYVI.DEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS
Retrocopy MAAHHRQKTAGRRKVQVSYVIQDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS

Parental  MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDRQ
          MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGF.MSTLRTHKDYVKALAYAKDKELVASAGLDR.
Retrocopy MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFFMSTLRTHKDYVKALAYAKDKELVASAGLDR*

Parental  IFLWDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHT
          IFL.DVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGH.
Retrocopy IFLLDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHM

Parental  DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTD
          DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQR.IATYRVHDEGVWALQVNDAFT.VYSGGRDRKIYCTD
Retrocopy DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRYIATYRVHDEGVWALQVNDAFTYVYSGGRDRKIYCTD

Parental  LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWILKGIHNFRASGDYDNDCTNPITPLC
          LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKW.LKGIHNFRASGDYDNDCTNPITPLC
Retrocopy LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWTLKGIHNFRASGDYDNDCTNPITPLC

Parental  TQPDQV
          TQPDQV
Retrocopy TQPDQV

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	28.20 RPM
SRP007412_cerebellum	0.00 RPM	34.17 RPM
SRP007412_heart	0.00 RPM	13.94 RPM
SRP007412_kidney	0.00 RPM	19.56 RPM
SRP007412_liver	0.00 RPM	13.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_320 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_320 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000007796	1 retrocopy	retro_pabe_1932,
Pongo abelii	ENSPPYG00000014001	2 retrocopies	retro_pabe_320 , retro_pabe_321,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,