RetrogeneDB ID: retro_pabe_300

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:137284999..137285916(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR82
• Ensembl ID: ENSPPYG00000013812
• Aliases: WDR82, WDR82P1
• Description: WD repeat domain 82 [Source:HGNC Symbol;Acc:28826]

Sequence

>retro_pabe_300
CTGCTGCGGAGCTTCTGTATCGCCAACGTGTTCCGCGAAAACTCGGACAAGATTAACTGCTTCAATTTCAGCCCTAACAG
CGAGGTGATCACCTCGAGCAGCAACGACGACTCCATCGTGCTCTATGACTGCCAGGAGGGCAAACCAAAACCCTGTTCAG
TAAGAAATACGGTGTGGCCTCATTAGATACACTCCTGCGGCAAACACGGTTGTTTACAGCTGTAACAAAATAGACGATAC
TATTCGTTACTTGTCCTTGCATGACAACAAATACATCAGATACTTTCCTGGACATAGCAAAAGGGTGGTGGTCTTGTCCA
TGTCACCTGTGGATGACACTTTCATTTCTGGGTCTCTTGAATGAGACCATTCGACTCTGGGATCTCCGGTCTCCCAACTG
CCAGGGCCTCATGCATATAAAGGGGAAGCCAGTTTGTTCTTTTGATCCAGAAGGGTGAATTTTTGCTGCTGGTGTCAACT
CTGAAACGGTCAAACTTTATGACCTTTGTTCTTTTGATAAGGGGCCATTTGCTACCTTTAAGATGCAGTATGATCGAACT
TGTGAGTGGACAGCACTTAAAATCAGCAACAGTGGCAAGGTCATCCTCATTTCCACCAACGTCAGCTTCATTCGTCTCAT
TGGTGCATTCAAAGGAGTGGTGATACACACATTTGGCCGTTATGCCAACAGCAAAGCTGTCACACTGGAGGCTTCATTTA
CTGCAGACTCTCAGTTTGTTATGGTTGGTTCAGAGGATGGCAAGATCCATTTCTGGAATGGAGAGAGCGGTATAAAAGTA
GTTGTGTTGGATGGTAAACACACAGGCCCAATTACCTGTTTGCAATTCAACCCCAAGTTTGTGACTTTTGCCAGCGGGTG
TACCAACACGGCCTTCTGGTTGCCCACCATTGATGAC

Alignment

ORF - retro_pabe_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.52 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTDSSFVAKVFRE-SDKINCFDFSPNGETVISSSDDDSIVLYDCQE-GKPKRTLYSKKYGV-DLIRYTHA
          L..S...A.VFRE.SDKINCF.FSPN.E...SSS.DDSIVLYDCQE.G..K.TL.SKKYGV..LIRYT.A
Retrocopy LLRSFCIANVFRENSDKINCFNFSPNSEVITSSSNDDSIVLYDCQE<GQTK-TLFSKKYGV<GLIRYTPA

Parental  ANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVVALSMSPVDDTFISGSLD-KTIRLWDLRSPNCQG
          ANTVVYS.NKIDDTIRYLSLHDNKYIRYFPGHSKRVV.LSMSPVDDTFISGSL...TIRLWDLRSPNCQG
Retrocopy ANTVVYSCNKIDDTIRYLSLHDNKYIRYFPGHSKRVVVLSMSPVDDTFISGSLE>ETIRLWDLRSPNCQG

Parental  LMHLQGKPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRTCEWTGLKFSNDGKLILIST
          LMH..GKPVCSFDPEG.IFAAGVNSE.VKLYDL.SFDKGPFATFKMQYDRTCEWT.LK.SN.GK.ILIST
Retrocopy LMHIKGKPVCSFDPEG*IFAAGVNSETVKLYDLCSFDKGPFATFKMQYDRTCEWTALKISNSGKVILIST

Parental  NGSFIRLIDAFKGVVMHTFGGYANSKAVTLEASFTPDSQFIMIGSEDGKIHVWNGESGIKVAVLDGKHTG
          N.SFIRLI.AFKGVV.HTFG.YANSKAVTLEASFT.DSQF.M.GSEDGKIH.WNGESGIKV.VLDGKHTG
Retrocopy NVSFIRLIGAFKGVVIHTFGRYANSKAVTLEASFTADSQFVMVGSEDGKIHFWNGESGIKVVVLDGKHTG

Parental  PITCLQFNPKFMTFASACSNMAFWLPTIDD
          PITCLQFNPKF.TFAS.C.N.AFWLPTIDD
Retrocopy PITCLQFNPKFVTFASGCTNTAFWLPTIDD

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	203.36 RPM
SRP007412_cerebellum	0.00 RPM	194.44 RPM
SRP007412_heart	0.03 RPM	59.21 RPM
SRP007412_kidney	0.00 RPM	75.08 RPM
SRP007412_liver	0.03 RPM	40.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_300 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_300 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_419
Macaca mulatta	retro_mmul_511
Callithrix jacchus	retro_cjac_3022

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300 ,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,