RetrogeneDB ID: retro_ptro_1054

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:46565128..46566689(-)
• Located in intron of: ENSPTRG00000007055

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL2A
• Ensembl ID: ENSPTRG00000007070
• Aliases: None
• Description: signal peptide peptidase like 2A [Source:HGNC Symbol;Acc:30227]

Sequence

>retro_ptro_1054
ATGGGGCCGCAGCGGCGGCTGTCCCCTGCCACGGCCGCCCTGCTCTGGGGCTCCCTGCTCCAGCTGACAGCCGCTCAGGA
AGCAATCTTGCATGCGTCTGGAAATGGCACATCCAAGGACTACTGCATGCTTTATAACCCCCATTGGTCAGCTCTTCCAA
GTACCCTAGAAAATGCAACTTCCATTAGTTTGATGAATCTGACTTCCGCACCACTATGCAACCTTTCTGATGTTCCTCCT
GTTGACATAAAGAACAAAGCAGTTGTGGTGCAATGGGGAAGCTGCCATTTTCTTGAAAACACCAGAATTGCACAGAAAAG
AGGTGCTGAAGCAATGTTGGTTGTCAATAACAGTATCCTATTTCCTACCTCAGGTAACAGATCTGAATTTCCTGATGTGA
AAATACTGATTGCATTTATAAGTGACAAAGACTTTATAGATATGAAGCAGACTCTAGGAAATAACATTACTGTGAAAATG
TATTCTCCATCGTGGCCTAACTTTGATTATACTATGGTGGTTATTTTTGTAATTGCTGTGTTCACTGTGGCATTAGGTGG
ATACTGGAGTGGACTAGTTGAATTGGAAAACTTGAAAGCAGTGACAACTGAAGATAGATAAATGAGGGGAAAAAAAGGAA
GAATATCTAACTTTTAGTCCTCTTACAGTTGTAATATTTGTGGTCATCTACTGTGTTATGATGGTCTTACTTTATTTCTT
CCACAAATGGTTAGTTTATGTTATGATAGCAATTTTCTGCATAGTATCAGCAATGAGTCTGTACAACTCTCTTGCTGCAC
TAATTCATAAGACACCATATGGACAATGCACAATTGAGTGTCGCGGCAAAAGCATGGAAGTGAGACTTATTTTTCTCTCT
GGACTGTGCATAGCAATAGCTATTGTTTGTGCTGTGTTTCAAAATGAAGACAGGTGGGCTTGGATTTTACAAGATATCTT
GGAGATTGCTTTCTGTCTGAATTTAATTAAAACACTGAAGTTGCCCAGCTTCAAGTCATGTGTGATACTTCTAGGCCTTC
TCCTCCTCTATGATGTATTTTTTGTTTTCATAACACCATTCATCACAAAGAATGGTGAGAGTATCATGGTTGAACTTGCA
GCTGGACCTTTTGAAAATACTGAAACATTGCCAGTAGTCATCAGAGTACCAAAGCTGATCTGTTTCTCAGTAATGAGTGT
GTGCATCATGCCTGTTTCAATATTGGGCTTTGGAGACATTATTGTACAGGCCTGTTGCTTGCGTACTGTAGAAGAGTTGA
TGTTTAGACTGGTTCTTCGTATATATACTATGTTTCCTCTACAGTTGCCTATGCTATTGGCATGATACTTAACATTTGTT
GTTCTGGTGCTGATGAAAAAGGGGCAACCTGCTCTCCTCTATTTAGTAACTTGCACACTTATTATTGCCTCAGTTGTTGC
CTGGAAATGTAAGGAAATGAAAAAGTTCTGGAAAGGTAACAGCTATCAGATGATGGACCATCTGTATTATGCAAAAAATG
AAGAAAACCCTGTGATGTCTGGTGAACAGATTGTCCAGCAA

Alignment

ORF - retro_ptro_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGPQRRLSPAGAALLWGFLLPLTAAQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTST
          MGPQRRLSPA.AALLWG.LL.LTAAQEAILHASGNGT.KDYCMLYNP.W.ALPSTLENATSISLMNLTS.
Retrocopy MGPQRRLSPATAALLWGSLLQLTAAQEAILHASGNGTSKDYCMLYNPHWSALPSTLENATSISLMNLTSA

Parental  PLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFI
          PLCNLSD.PPV.IK.KAVVV.WGSCHFLE..RIAQK.GAEAMLVVNNS.LFP.SGNRSEFPDVKILIAFI
Retrocopy PLCNLSDVPPVDIKNKAVVVQWGSCHFLENTRIAQKRGAEAMLVVNNSILFPTSGNRSEFPDVKILIAFI

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

Parental  KKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIA
          .KKEEYLTFSPLTVVIFVVI.CVMMVLLYFF.KWLVYVMIAIFCI.SAMSLYN.LAALIHK.PYGQCTI.
Retrocopy EKKEEYLTFSPLTVVIFVVIYCVMMVLLYFFHKWLVYVMIAIFCIVSAMSLYNSLAALIHKTPYGQCTIE

Parental  CRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLL
          CRGK.MEVRLIFLSGLCIA.A.V.AVF.NEDRWAWILQDIL.IAFCLNLIKTLKLP.FKSCVILLGLLLL
Retrocopy CRGKSMEVRLIFLSGLCIAIAIVCAVFQNEDRWAWILQDILEIAFCLNLIKTLKLPSFKSCVILLGLLLL

Parental  YDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIV-PGL
          YDVFFVFITPFITKNGESIMVELAAGPF.N.E.LPVVIRVPKLI.FSVMSVC.MPVSILGFGDIIV..GL
Retrocopy YDVFFVFITPFITKNGESIMVELAAGPFENTETLPVVIRVPKLICFSVMSVCIMPVSILGFGDIIV<TGL

Parental  LIAYCRRFDVQTGSSYIYYVSSTVAYAIGMI-LTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMK
          L.AYCRR.DV.TGSSYIYYVSSTVAYAIGMI.LTFVVLVLMKKGQPALLYLV.CTLI.ASVVAW..KEMK
Retrocopy LLAYCRRVDV*TGSSYIYYVSSTVAYAIGMI>LTFVVLVLMKKGQPALLYLVTCTLIIASVVAWKCKEMK

Parental  KFWKGNSYQMMDHLDYATNEENPVISGEQIVQQ
          KFWKGNSYQMMDHL.YA.NEENPV.SGEQIVQQ
Retrocopy KFWKGNSYQMMDHLYYAKNEENPVMSGEQIVQQ

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	0.07 RPM	2.59 RPM
SRP007412_cerebellum	0.11 RPM	3.44 RPM
SRP007412_heart	0.17 RPM	33.90 RPM
SRP007412_kidney	0.29 RPM	29.94 RPM
SRP007412_liver	0.10 RPM	35.97 RPM
SRP007412_testis	0.63 RPM	8.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1054 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1054 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1566
Gorilla gorilla	retro_ggor_1191
Pongo abelii	retro_pabe_1293

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 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	ENSPPYG00000006472	1 retrocopy	retro_pabe_1293,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275,
Pan troglodytes	ENSPTRG00000007070	1 retrocopy	retro_ptro_1054 ,
Rattus norvegicus	ENSRNOG00000011652	1 retrocopy	retro_rnor_1750,