RetrogeneDB ID: retro_pabe_1802

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:7794620..7795250(-)
• Located in intron of: ENSPPYG00000010712

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC84
• Ensembl ID: ENSPPYG00000003948
• Aliases: None
• Description: coiled-coil domain containing 84 [Source:HGNC Symbol;Acc:30460]

Sequence

>retro_pabe_1802
TCTCCCCAGGATTATGCACGATTCAAAAAATCCCTGGTGGAAGACTTGGGTTCCTATGAAGAAAAAGAGGATGAGGTGAC
CAAGGAGATGGCAACTCAGATCCGTGAGGTGGAAGAGAGCTGGCAGGAGGTGGTTCAGTCTGTCTTAGAGGTTGGTTTCC
CTCGGAGGATCCAGACCCCCTTAGCCAGTGCCAGGCACTTTAGTCCCTGGAAGCTGGAAAAGGATGAACAGCCAAGTAGC
TTCCAGCTCACAGCAGCCCTCCAACTCGGACCTGCCACAGCTCCAGAGCTTGACTGGATGGAGACAGGACAATCTCTGAT
ATTCATTGGCCATCAGGATATACCAGGAGCTGGGAACATCCACTCAGGTGCCACACCTCCCTGGATGATCCAAGATAAAG
AATGCATCTCTGGGAACCAACAAACAGGACGGTCCTAAAAATAATTTATTAAAGAAAAGGAAAAAGAGAAGTTGAAGGAA
CTTTCCCCAAACTGAGTTGGGGCCAATTTTGATCACAGCTAAAGGACCAGTGCAGGCTGGCTGCCCTCTTTGGACCGTGT
CTGGAATAATGGATACTGCTGGCAGTTCAGGCATCAGCTCAGAACTGAAGCTGCAGCAATGAACAAGCAG

Alignment

ORF - retro_pabe_1802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 61.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPQDYARFKKSMVKGLDSYEEKEDEVIKEMAAQIREVEQSRQEVVRSVLE---PQTVPDPEEGSSAHGSW
          .PQDYARFKKS.V..L.SYEEKEDEV.KEMA.QIREVE.S.QEVV.SVLE...P.....P.........W
Retrocopy SPQDYARFKKSLVEDLGSYEEKEDEVTKEMATQIREVEESWQEVVQSVLEVGFPRRIQTPLASARHFSPW

Parental  KGINSQVASSSQQPANLDLPP--APELDWMETGPSLTFIGHQDIPGVGNIHSGATPPWMIQD-EYTAGNQ
          K.......SS.Q..A.L.L.P..APELDWMETG.SL.FIGHQDIPG.GNIHSGATPPWMIQD.E...GNQ
Retrocopy KLEKDEQPSSFQLTAALQLGPATAPELDWMETGQSLIFIGHQDIPGAGNIHSGATPPWMIQDKECISGNQ

Parental  EIGPSYEEFLKEKEKQKLKKLPPDRVGANFDHSSRTSAGWLPSFGRVWNNGRRWQSRHQFKTEAAAMKKQ
          ..G.S...F.KEKEK.KLK.L.P..VGANFDHS.RTSAGWLPS..RVWNNG..WQ.RHQ..TEAAAM.KQ
Retrocopy QTGRS*K*FIKEKEKEKLKELSPN*VGANFDHS*RTSAGWLPSLDRVWNNGYCWQFRHQLRTEAAAMNKQ

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	2.76 RPM
SRP007412_cerebellum	0.00 RPM	4.86 RPM
SRP007412_heart	0.03 RPM	1.11 RPM
SRP007412_kidney	0.00 RPM	3.78 RPM
SRP007412_liver	0.00 RPM	3.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1802 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1802 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2451
Pan troglodytes	retro_ptro_1416
Gorilla gorilla	retro_ggor_1527

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186166	1 retrocopy	retro_hsap_2451,
Gorilla gorilla	ENSGGOG00000023065	1 retrocopy	retro_ggor_1527,
Nomascus leucogenys	ENSNLEG00000007378	1 retrocopy	retro_nleu_205,
Pongo abelii	ENSPPYG00000003948	1 retrocopy	retro_pabe_1802 ,
Pan troglodytes	ENSPTRG00000004360	1 retrocopy	retro_ptro_1416,