RetrogeneDB ID: retro_pabe_3790

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:90224601..90225202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSPPYG00000001256
• Aliases: None
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_pabe_3790
CCCATGGAGGTTAAGAAAGAAGGAATAAGGTGAATTGGAAGAAGATCCAATCAACAACTGCAAGGTGAAGGGAAAATAAT
TGAGATAGGATGGGGAAAGGCAACCACCTTATGAAGGAAGATTTGAAAAACCACTTGAAAAGGGTGAAAGAGGAAACTTT
TTATTTGATAGACCTATCATTGAGCAACACATTCGAGGCTGTGGTGGCCTTGGAAGAAGTAGAGAGGGCTGTCAAAGTGA
AATGGGCCAAGGGTATGGATTTGATTTTTATGGTAAATGTGAATTTGATAAGCATGCTGGTAGGCAGGCTGGAAGGCATA
GATCTGGACTGAAGCACAAGGACAAACATGGAGGTAGTGGATTTTACAACTGGGGAACTGTAAAAGATAAGTTAATTGAC
TTGGATTAATCAAATATGACCTAGGAAACACCTGAAGGTGAAGAATTTCCAGTGGCAGACACTGCAAATAAGGAGAAGGA
TGTTTAAGAGGTAAAAAAAGAGGGTCCAAAAGAGATGACTCTGGATAAGTGGAATGCTATTCAAAATAAGGACTGGCCAA
AAGTAGAATTTAATATCCAAAAACAAAACAAAGGTACTGAT

Alignment

ORF - retro_pabe_3790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 53.4 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVALKKEGIRRVGRRPDQQLQGE-GKIIDRRPERRPPRERRFEKPLEEKGEGGEFSVDRPIIDRPIRGRG
          P...KKEGIR..GRR..QQLQGE.GK......ER.PP.E.RFEKPLE.KGE.G.F..DRPII...IRG.G
Retrocopy PMEVKKEGIR*IGRRSNQQLQGE>GK*LR*DGERQPPYEGRFEKPLE-KGERGNFLFDRPIIEQHIRGCG

Parental  GLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGLKHEDKRGGSGSHNWGTVKDELTDLDQ
          GLGR.R.G....MG.G.GFD..GK.EFD.H.G..R....H.SGLKH.DK.GGSG..NWGTVKD.L.DLD.
Retrocopy GLGRSREGCQSEMGQGYGFDFYGKCEFDKHAG--RQAGRHRSGLKHKDKHGGSGFYNWGTVKDKLIDLD*

Parental  SNVTEETPEGEEHHPVADTENKENEVEEVKEEGPKEMTLDEWKAIQNKDRAKVEFNIRKPNEGAD
          SN.T.ETPEGEE..PVADT.NKE..V.EVK.EGPKEMTLD.W.AIQNKD..KVEFNI.K.N.G.D
Retrocopy SNMT*ETPEGEEF-PVADTANKEKDV*EVKKEGPKEMTLDKWNAIQNKDWPKVEFNIQKQNKGTD

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	48.66 RPM
SRP007412_cerebellum	0.00 RPM	35.14 RPM
SRP007412_heart	0.00 RPM	54.58 RPM
SRP007412_kidney	0.00 RPM	69.84 RPM
SRP007412_liver	0.00 RPM	55.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3790 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3790 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207, retro_cjac_3015,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Oryctolagus cuniculus	ENSOCUG00000008946	1 retrocopy	retro_ocun_1041,
Pongo abelii	ENSPPYG00000001256	1 retrocopy	retro_pabe_3790 ,
Sorex araneus	ENSSARG00000000803	1 retrocopy	retro_sara_135,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331, retro_tbel_2427, retro_tbel_532,