RetrogeneDB ID: retro_pabe_1293

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:45899731..45901292(-)
• Located in intron of: ENSPPYG00000006463

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL2A
• Ensembl ID: ENSPPYG00000006472
• Aliases: None
• Description: signal peptide peptidase like 2A [Source:HGNC Symbol;Acc:30227]

Sequence

>retro_pabe_1293
ATGGGGCCGCAGCGGCGGCTGTCCCCTGTCACGGCCGCCCTGCTCTGGGGCTTCCTGCTCCAGCTGACAGCCGCTCAGGA
AGCAATCTTGCATGCGTCTGGAAATGGCACATCCAAGGACTACTGCATGCTTTATAACCCCCATTGGTCAGCTCTTCCAA
ATACCCTAGAAAATGCAACTTCCATTAGTTTGATGAATCGGACTTCCGCACCACTATGCAACCTTTCTGATGTTCCTCCT
GTTGACATAAAGAACAAAGCAGTTGTGGTGCAATAGGGAAGCTGCCATTTTCTTGAACACACCAGAATTGCACAGAAAAG
AGGTGCTGAAGCAATGTTGGTTGTCAATAACAGTATCCTATTTCCTACATCAGGTAACAGATCTAAATTTCCTGATGTGA
AAATACTGATTGCATTTATAAGCCACAAAGACTTTAAAGATATGAAGCAGACTCTAGGAAATAACATTACTGTGAAAATG
TATTCTCCATCATGGCCTAACTTTGATTATACTATGGTGGTTATTTTTGTAATTGCTGTGTTCACTGTGGCATTAGGTGG
ATACTGGAGTGGACTAGTTGAATTGGAAAACTTGAAAGCAGTGACAACTGAAGATAGATAAATGAGGGGAAAAAAAGGAA
GAATATCTAACTTTTAGTCCTCTTACAGTTGTAATATTTGTGGTCATCTACTGTGCTATGATGGTCTTACTTTATTTCTT
CTACAAATGGTTAGTTTATGTTATGATAGCAATTTTCTGCATAGTATCAGCAATGAGTCTGTACAACTCTCTTGCTGCAC
TAATTCATAAGATACCATATGGACAATGCACAATTGAGTATCGTGGCAAAAGCATGGAAGTGAGACTTATTTTTCTCTCT
GGTCTGTGCATAGCAATAGCTATTGTTTGGGCTGTGTTTCGAAATGATGACAGGTGGGCTTGGATTTTACAAGATATCTT
GGGGATTGCTTTCTGTTTGAATTTAATTAAAACACTGAAGTTGCCCAGCTTCAAGTCATGTGTGATACTTCTAGGCCTTC
TCCTCCTCTATGATGTACTTTTTGTTTTCATAACACCATTCATCACAAAGAATGGTGAGAGTATCATGGTTGAAATTGCA
GCTGGACCTTTTGAAAATACTGAAACATTGCCAGTAGTCATCAGAGTACCAAAGCTGATCTGTTTCTCAGTAATGAGTGT
GTGCATCATGCCTGTTTCAATATTGGGCTTTGGAGACATTATTGTACAGCCCTGTTGATTGCGTACTGTAGAAGAGTTGA
TGTTTAGACTGGTTCTTCATATATATACTATGTTTCCTCTACAGTTGCCTATGCTATTGGCATGACACTTACATTTGTTG
TTCTGGTGCTGATGAAAAAGGGGCAACCTGCTCTCCTCTTATTTAGTAACTTGCACACTTATTATTGCCTCAGTTGTTGC
CTGGAAATCTAAGGAAATGAAAAAGTTCTGGAAAGGTAACAGCTATCAGATGATGGACCATCTGTATTATCCAAAAAATG
AAGAAAACCCTGTGATGTCTGCTGAACAGATTGTCCAGCAA

Alignment

ORF - retro_pabe_1293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGPQRRLSPAGAVLLWGFLLPLTAAQEAILHASGNSTTKDYCMLYNPYWTALPSTLENATSISLMNLTST
          MGPQRRLSP..A.LLWGFLL.LTAAQEAILHASGN.T.KDYCMLYNP.W.ALP.TLENATSISLMN.TS.
Retrocopy MGPQRRLSPVTAALLWGFLLQLTAAQEAILHASGNGTSKDYCMLYNPHWSALPNTLENATSISLMNRTSA

Parental  PLCNLSDIPPVGIKNKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFI
          PLCNLSD.PPV.IKNKAVVV..GSCHFLE..RIAQK.GAEAMLVVNNS.LFP.SGNRS.FPDVKILIAFI
Retrocopy PLCNLSDVPPVDIKNKAVVVQ*GSCHFLEHTRIAQKRGAEAMLVVNNSILFPTSGNRSKFPDVKILIAFI

Parental  SYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMR-
          S.KDF.DM.QTLG.NITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDR.MR.
Retrocopy SHKDFKDMKQTLGNNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDR*MR>

Parental  KKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIA
          .KKEEYLTFSPLTVVIFVVI.C.MMVLLYFFYKWLVYVMIAIFCI.SAMSLYN.LAALIHKIPYGQCTI.
Retrocopy EKKEEYLTFSPLTVVIFVVIYCAMMVLLYFFYKWLVYVMIAIFCIVSAMSLYNSLAALIHKIPYGQCTIE

Parental  CRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLL
          .RGK.MEVRLIFLSGLCIA.A.VWAVFRN.DRWAWILQDILGIAFCLNLIKTLKLP.FKSCVILLGLLLL
Retrocopy YRGKSMEVRLIFLSGLCIAIAIVWAVFRNDDRWAWILQDILGIAFCLNLIKTLKLPSFKSCVILLGLLLL

Parental  YDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIV-PGL
          YDV.FVFITPFITKNGESIMVE.AAGPF.N.E.LPVVIRVPKLI.FSVMSVC.MPVSILGFGDIIV...L
Retrocopy YDVLFVFITPFITKNGESIMVEIAAGPFENTETLPVVIRVPKLICFSVMSVCIMPVSILGFGDIIV<TAL

Parental  LIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALL-YLVPCTLITASVVAWRRKEMK
          LIAYCRR.DV.TGSSYIYYVSSTVAYAIGM.LTFVVLVLMKKGQPALL.YLV.CTLI.ASVVAW..KEMK
Retrocopy LIAYCRRVDV*TGSSYIYYVSSTVAYAIGMTLTFVVLVLMKKGQPALL>YLVTCTLIIASVVAWKSKEMK

Parental  KFWKGNSYQMMDHLDYATNEENPVISGEQIVQQ
          KFWKGNSYQMMDHL.Y..NEENPV.S.EQIVQQ
Retrocopy KFWKGNSYQMMDHLYYPKNEENPVMSAEQIVQQ

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	1.94 RPM
SRP007412_cerebellum	1.22 RPM	5.84 RPM
SRP007412_heart	0.24 RPM	11.20 RPM
SRP007412_kidney	0.60 RPM	8.49 RPM
SRP007412_liver	1.35 RPM	13.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1293 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1293 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1566
Pan troglodytes	retro_ptro_1054
Gorilla gorilla	retro_ggor_1191

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008946	1 retrocopy	retro_dord_754,
Homo sapiens	ENSG00000138600	1 retrocopy	retro_hsap_1566,
Gorilla gorilla	ENSGGOG00000013154	1 retrocopy	retro_ggor_1191,
Pongo abelii	ENSPPYG00000005041	2 retrocopies	retro_pabe_1578, retro_pabe_1579,
Pongo abelii	ENSPPYG00000006472	1 retrocopy	retro_pabe_1293 ,
Pan troglodytes	ENSPTRG00000007070	1 retrocopy	retro_ptro_1054,
Rattus norvegicus	ENSRNOG00000011652	1 retrocopy	retro_rnor_1750,