RetrogeneDB ID: retro_pabe_2516

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:55284312..55285540(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPP3
• Ensembl ID: ENSPPYG00000003023
• Aliases: None
• Description: dipeptidyl peptidase 3 [Source:RefSeq peptide;Acc:NP_001125322]

Sequence

>retro_pabe_2516
AGGGGCCTCTGGCAGACCTGCGGGGAGTTTATGTTCTCTCTGGAGTCAAGGCTTCGACACCTTGGGCTGGGGAAGGAGGG
AATCACCACCTATTTCCCCTGGAATTGTACCATGGAAGATGCCAAACTGGCTTAAGAGTTTCTGGACTCACAGAACCTCA
GATCCTACAACACCTGGCTCTTCAAAGAGGTTGACAGAGAAGGGAAGCCCCACTATGAGGTGTGGCTGGCTTCTGTACTC
CGCACAGAGCCTTCCCTGCACTCCGAGGTGACTTCCAGGCTGAAGAGCTACGAATTCCGGGGAAGCACTTTCCAGGTGAC
CCAGGGGGACTAAGCACTCATCCTCCAGAAGGTGGTGGAGCAGCTGGATAAAGCCAAGGCATATGCAGCCAACAGCCACC
AGGGGGAGATGCTGGCCCAGTATATACAGTGCTTCACCCAGGGCTCCATCGAGGCCCATAAGAGGGGCTCCTGCTTCTGG
AGCCGGGACAAAAGCCCCATCATGGAGAGTTACATCAGGTTCATCGAGAGCTACCATGACCCCTTTGGTTCCGTAGGAGA
ATTTGAAGGCTTCGTAGCCATAGTGAACAAGACCGTGAGCGCCAAGATTGAGCGGCTGGTGGCGAGCGCAGAGCATCTGC
TGAAGATGCCGCCCTGGCCCCAAGTCTTTGAGAAGGACAAGTTCCTCACCCCTGACTTCACCTCCCAGGATGGTCTTGCC
TTCGCTGGTTCTGGCATCCCTGCTGGCATCAACATCCCCAACTACGATGTCCTGAAGCAGATGTAAGGCTTTAAGAATGT
GTCGCTTGTGAACGTGCCGGCTGTGGCCTAGGCCACACAGCAGGATAAGCTCACCTTCCTGGAGGAGGATGACAAGGACC
TGTACATCCTCTGGAAGGGGCCCTCCTTCGATGTGCAGGTGGGCCTGAACGAGCTGCTGGGCCATGGCAGCGGCAAGCTC
TTCGTGCAGGATGAAAAAGTAGCATTCAACTTTGACCAGGAGACAGTGATCAACCCAGAGACTGGTGAGCAGATTCAGAG
ATGGTATCCGAGCGGGGAGACCTGGGACAACAAGTTCAGCACCATCGCCTCCAGCTATGAAGAGTACCGGGCTGAGAGAG
AGTGGGTCTCTTCCTCTGTCTCCCCCACAAGTGTTGGAGATCCATGGTTTCGAGGGGGCTGATGCGGAGGACGTGATCTA
CGTGGACTGGCTTCACATGGTTCGTTCC

Alignment

ORF - retro_pabe_2516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.95 %
• Parental protein coverage: 55.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGEGKP
          RGLWQTCGE.MFSLE.RLRHLGLGKEGITTYF..NCTMEDAKLA..FLDSQNL..YNT.LFKEVD.EGKP
Retrocopy RGLWQTCGEFMFSLESRLRHLGLGKEGITTYFPWNCTMEDAKLA*EFLDSQNLRSYNTWLFKEVDREGKP

Parental  HYEVRLASVLGSEPSLDSEVTSKLKSYKFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQ
          HYEV.LASVL..EPSL.SEVTS.LKSY.FRGS.FQVT.GD.A.ILQKVVEQL.KAKAYAANSHQG.MLAQ
Retrocopy HYEVWLASVLRTEPSLHSEVTSRLKSYEFRGSTFQVTQGD*ALILQKVVEQLDKAKAYAANSHQGEMLAQ

Parental  YIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASA
          YI..FTQGSIEAHKRGS.FW..DK.PI.ESYI.FIESY.DPFGS.GEFEGFVA.VNK..SAK.ERLVASA
Retrocopy YIQCFTQGSIEAHKRGSCFWSRDKSPIMESYIRFIESYHDPFGSVGEFEGFVAIVNKTVSAKIERLVASA

Parental  EQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQ
          E.LLK..PWP..FEKDKFLTPDFTS.D.L.FAGSGIPAGINIPNYD.L.Q..GFKNVSL.NV.AVA.ATQ
Retrocopy EHLLKMPPWPQVFEKDKFLTPDFTSQDGLAFAGSGIPAGINIPNYDVLKQM*GFKNVSLVNVPAVA*ATQ

Parental  REKLTFLEEDDKDLYILWKGPSFDVQVGLHELLGHGSGKLFVQDEKGSFNFDQETVINPETGEQIQSWYL
          ..KLTFLEEDDKDLYILWKGPSFDVQVGL.ELLGHGSGKLFVQDEK..FNFDQETVINPETGEQIQ.WY.
Retrocopy QDKLTFLEEDDKDLYILWKGPSFDVQVGLNELLGHGSGKLFVQDEKVAFNFDQETVINPETGEQIQRWYP

Parental  SGETWDSKFSTIASSYEECRAESVGLYLCLHP-QVLEIFGFEGADAEDVIYVNWLNMVRA
          SGETWD.KFSTIASSYEE.RAE.........P.QVLEI.GFEGADAEDVIYV.WL.MVR.
Retrocopy SGETWDNKFSTIASSYEEYRAEREWVSSSVSP>QVLEIHGFEGADAEDVIYVDWLHMVRS

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	8.35 RPM
SRP007412_cerebellum	0.00 RPM	4.86 RPM
SRP007412_heart	0.00 RPM	1.48 RPM
SRP007412_kidney	0.00 RPM	19.09 RPM
SRP007412_liver	0.00 RPM	9.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2516 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000003023	1 retrocopy	retro_pabe_2516 ,
Rattus norvegicus	ENSRNOG00000031485	2 retrocopies	retro_rnor_1833, retro_rnor_2611,