RetrogeneDB ID: retro_pabe_3162

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:92629212..92629718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSPPYG00000019477
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_pabe_3162
ATGGTGACAAAACCCAAAGCAGTGACAATACCAGCTCCAGCTACAACGCAGCAATCAAATCCTGCCACTGCTATGAAGTG
AGTTCCTCCTCAGCAGCTGCTGTGGCTTAGCCTGCAACCCTCATCTCTGCCTTTGCTCCCACATCCACACCTATATCTAT
CACCCCAGCACCAACAACAGCATGTCCTGAACATGTACCTTCTAGTGCAATGAAACAAGATAAACCTGGAGAAAAGTCAG
CAGAAACACCAGTGGCTACTAGCTCAGCATCAACTGAGAGTAGAGCAGGGGATTCTTCTCTGCCAAACCTTTTTGAAGTT
GCAAGTACACTTGTAAAAGGTCAGTCCTATGAGAATATGGTAACTGAGGTCATGTCAATGGGCTATAAACAAGAGCAAGC
AATTGTGGCCCTGAGAGTCATTTTCAACAATCCTGACAGAGGAGTGCAGTATCTTTTAATAGGAATCCCTGGAGGTAGAA
AAAGTCAGGCTGTGGTTGAGCACCCC

Alignment

ORF - retro_pabe_3162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.5 %
• Parental protein coverage: 50.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVTKPKAVSTPAPATTQQSAPASTTA-VTSSTTTTVAQAPTPVPALAPTSTPASITPASATASSEPASAS
          MVTKPKAV..PAPATTQQS.PA.....V.SS....VA...T...A.APTSTP.SITPA..TA..E....S
Retrocopy MVTKPKAVTIPAPATTQQSNPATAMK<VSSSSAAAVA*PATLISAFAPTSTPISITPAPTTACPEHVPSS

Parental  AAKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAAL
          A.KQ.KP.EK.AETPVATS...T.S..GDSS..NLFE.A.S.LV.GQSYENMVTE.MSMGY..EQ.I.AL
Retrocopy AMKQDKPGEKSAETPVATSSASTESRAGDSSLPNLFEVA-STLVKGQSYENMVTEVMSMGYKQEQAIVAL

Parental  RASFNNPDRAVEYLLMGIPGDRESQAVVDPP
          R..FNNPDR.V.YLL.GIPG.R.SQAVV..P
Retrocopy RVIFNNPDRGVQYLLIGIPGGRKSQAVVEHP

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	96.10 RPM
SRP007412_cerebellum	0.00 RPM	107.50 RPM
SRP007412_heart	0.00 RPM	63.79 RPM
SRP007412_kidney	0.00 RPM	66.86 RPM
SRP007412_liver	0.00 RPM	84.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3162 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3162 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3754
Macaca mulatta	retro_mmul_1725

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162 ,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,