RetrogeneDB ID: retro_pabe_1818

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:28407962..28409450(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5RAP3
• Ensembl ID: ENSPPYG00000008888
• Aliases: None
• Description: CDK5 regulatory subunit associated protein 3 [Source:HGNC Symbol;Acc:18673]

Sequence

>retro_pabe_1818
CCCATCGACATCCAGACCAGCAAGCTGCTCGATTGGCTGGTGGACAGAAGGCACTGCAGCCTGAAATGGCAGAGTCTGGT
GCTGACGATCCGAGAGAAGATCAATGCTGCCATCCAGGACAAGCCAGAGAGCGAAGAGATCGCACAGCTGCTGTCTGGGT
CCTACATTCACTATTTTCACTGCCTAAGAATCCTGGACCTTCTCAAAGGCACAGAGGCCTCCGCGAAAAATATTTTTGGC
CAATACTCTTCACAGCAGATGAAGGATTGGCAGGAGATTATAGCCCTATATGAGAAGAACAACACCTACTTAGTGGAACT
CTCTAGCCTCCTGGTTCAGAATGTCAACTATGAGATCCCCTCACTGAAGAAGCAGATTGCCAAGTGCCAGCAGCTGCAGC
AAGAATACAGCCACAAGGAGGAGGAGTGCCAGGCAGTGCCTGCCGAGATGTGGGAGCAGTTCTACCACTCCTGCAAGCAG
TATGGCATCACGGGTGAAAATGTTCGAGGAGAACTGCTGGCCCTGGTGAAGGACCTGCCGAGTCAGCTGGCTGAGATTGG
GGCAGTGTCTCAGCAGTCCCTGGGGGAAGCCATTGACGTGTACCAGGCCTCTGTGGGGTTTGTGTGTGAGAGCCCCACAG
AGCAGGTGTTGCCAATGCTGCGGTTCATGCAGAAGCGGGGAAACTCAATGGTGTACGAGTGGAGGACAGTGACAGAGCCC
TCTGTGGTGGAGCGACCCCACCTCGAGGAGCTTCCTGAGCAGGTGGCAGAAGACGCGATTGACTGGGGCGACTTTGGGGT
AGAGGCAGTGTCTGAGGGGACTGACTCTGGCATCTCTGCCGAGGCTGCTGGAATCAACTGGGGCATCTTCCCGGAATCAG
ATTCAAAGGACCCTGGAGGTGACTGGGGAGACGATGCTGTTGCTTTGCAGATCACAGTGCTGGAAGCAGGAACCCAGGCT
CCAGAATGTGTTGCCAGGGGCCCAGATGCTCTGACACTTCTTGAATACACTGAGACCCGGAATCAGTTCCTTGATGAGCT
CATGGCGCTTGAGATCTTCTTAGCCCAGAGAGCAGTGGAGTTGAGTGAGGAGGCAGATGTCCTGTCTGTGAGCCAGTTCC
AGCTGGCTCCAGCCATCCTGCAGGGCCAGACCAAAGAGAAGATTGTTACCATGGTGTCAGTGCTAGAGGATCTGATTGGC
AAGCTTACCAATCTTCAACTGCAACACCTGTTTTTGACCCTGGCCTCACAAAGGTATGTGGACTGAGTGACTGAATTCCT
CCAGCAAAAGCTGAAGCAGTCCCAGCTGCTGGCTTTGAAGAAAGAGCGGATGGTGCAGAAGCAGCAGGAGGCAATTGAGG
AGCAGGTGGCTCTGGAGCCTAAGCTGGACCTGCTGCTGGAGAAGACCAAGGAGCTGCAGAAGCTGATTGAAGCTGACATC
TCCAAGAGGTACAGCGGGCGCCCTGTGAACCTGATGGGAACCTCTCTG

Alignment

ORF - retro_pabe_1818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSGSYIHYFHCLRILDLLKG
          PIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQD.PESEEIAQLLSGSYIHYFHCLRILDLLKG
Retrocopy PIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDKPESEEIAQLLSGSYIHYFHCLRILDLLKG

Parental  TEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELSSLLVRNVNYEIPSLKKQIAKCQQLQQEYSRKE
          TEAS.KNIFG.YSSQ.MKDWQEIIALYEK.NTYLVELSSLLV.NVNYEIPSLKKQIAKCQQLQQEYS.KE
Retrocopy TEASAKNIFGQYSSQQMKDWQEIIALYEKNNTYLVELSSLLVQNVNYEIPSLKKQIAKCQQLQQEYSHKE

Parental  EECQAGAAEMREQFYHSCKQYGIMGENVRGELLALVKDLPSQLAEIGAAAQQSLGEAIDVYQASVGFVCE
          EECQA..AEM.EQFYHSCKQYGI.GENVRGELLALVKDLPSQLAEIGA..QQSLGEAIDVYQASVGFVCE
Retrocopy EECQAVPAEMWEQFYHSCKQYGITGENVRGELLALVKDLPSQLAEIGAVSQQSLGEAIDVYQASVGFVCE

Parental  SPTEQVLPMLQFVQKRGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISA
          SPTEQVLPML.F.QKRGNS.VYEWRT.TEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISA
Retrocopy SPTEQVLPMLRFMQKRGNSMVYEWRTVTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISA

Parental  EAAGIDWGIFPESDSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETRNQFLDEL
          EAAGI.WGIFPESDSKDPGGD...WGDDAVALQITVLEAGTQAPE.VARGPDALTLLEYTETRNQFLDEL
Retrocopy EAAGINWGIFPESDSKDPGGD---WGDDAVALQITVLEAGTQAPECVARGPDALTLLEYTETRNQFLDEL

Parental  MELEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKTVTMVSVLEDLIGKLTSLQLQHLFMILASP
          M.LEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEK.VTMVSVLEDLIGKLT.LQLQHLF..LAS.
Retrocopy MALEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKIVTMVSVLEDLIGKLTNLQLQHLFLTLASQ

Parental  RYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTKELQKLIEADISKRYSGR
          RYVD.VTEFLQQKLKQSQLLALKKE.MVQKQQEA.EEQ.ALEPKLDLLLEKTKELQKLIEADISKRYSGR
Retrocopy RYVD*VTEFLQQKLKQSQLLALKKERMVQKQQEAIEEQVALEPKLDLLLEKTKELQKLIEADISKRYSGR

Parental  PVNLMGTSL
          PVNLMGTSL
Retrocopy PVNLMGTSL

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	36.99 RPM
SRP007412_cerebellum	0.00 RPM	48.52 RPM
SRP007412_heart	0.00 RPM	12.70 RPM
SRP007412_kidney	0.00 RPM	46.94 RPM
SRP007412_liver	0.00 RPM	34.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1818 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1818 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108465	1 retrocopy	retro_hsap_2466,
Gorilla gorilla	ENSGGOG00000022994	1 retrocopy	retro_ggor_1535,
Nomascus leucogenys	ENSNLEG00000002109	1 retrocopy	retro_nleu_2448,
Ochotona princeps	ENSOPRG00000004107	2 retrocopies	retro_opri_276, retro_opri_480,
Pongo abelii	ENSPPYG00000008888	1 retrocopy	retro_pabe_1818 ,
Pan troglodytes	ENSPTRG00000009345	1 retrocopy	retro_ptro_1425,