RetrogeneDB ID: retro_ptro_3117

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:63950447..63952193(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHC1
• Ensembl ID: ENSPTRG00000001397
• Aliases: None
• Description: None

Sequence

>retro_ptro_3117
ATGAATCTCCTGCCCCCCAAGTCCAAGTGCAATCCACTGTGGAATGAGTCTCTGTCATCGCTGGAGGAGGGGCCTTCAGG
GTCCACCCCACCAGAGGAGCTGCCTTCCCCATCAGCCTCATCCCTGGGGCCCATCCTGCCCCCTCTGCCTGGGAACCATA
GTCCCACTACCCTGTGCTCCTTCTTCCCCTGGATGAGCAACCTGAGGCTGGCCAATTGGGCCGGGGGACACCTGGGGCCT
AAGGGGGAGCCAGGAAGGGCAGCCAATGATGGGGAGGGCATTGTAGGGGCAACCATGCCAGACTCATTCCCCTACCCCTC
CTCCAGGACATGAACAAGCTGAGTGGAGGTGGTGGGTGCAGGACTCAGGTGGAAGGGGGCCAGCTGGGGGGTGAGGAGTG
GACCCGCCGTGGGAGCTTTGTCAATAAGCCCATGTGGGGCTAGCTGCATCCCAATGACAAAGTCACGAGACCTGGGGTTT
CCTACTTGATTTGGTACATGGGCTGTGTGGAGATCCTGCAGTCAATGAGTGCCCTGGACTTCAACACCTGGACTCAGGTC
ACCAGGGAGGCCATCAGTCTTGTGTGTGAGGCTGTGCCAGGTGCCAAGGGGGTGACAAGGAGGAGAAAGCCCTGTAACCA
TCCACTCAGCTCTATCCTGGGAAGGAGTAACCTGAAATTTGCTGCAATGACAATCACTCTCACCATCTCCACCAGCAGCC
TCAACGTCATGGTTGCAGACTGCAAACAGATTATCACTAACCACCATATGCAATCTATCTCATTTACATCCAGTGGGGAT
CCAGACACAGCCAAGTATGTCGCCAACGTTGCCAAAGACCCTGTGAGTCAGAAAGCATGCCACATTCTGGAGTGTCCTGA
AGGGCTTGCTCAGGATGTCATCAGCACCATTGGCCAGGCCTTCAAGTTGCACTTTAAACAATACCTCAGAAAACCACCCA
AACTGGTCACCCCCCATGACAGGATGACTGGCTTTCATGGCTTAGCTTGGGATGAGGAGGAGGAAGAGCCACCTGGCCAT
CAGCACTATAATGACTTCCTGGGAAGGAATCCCCTCTTTGGCATGTGGTATACATGAGGCTTCGGGAAGGAGCCACTCCA
GGGGCTGCTCGACCCACTCCACCCAGTGCCCAGACCCCCAGCCACTTGGGATCTACACTGCCTGTAGGACAGTCTGTTGG
GGGAGATCCAGAAGTTTGCAAATAGATGCCACCTCCACCACCCTGTCCAGGCAGAGAGCTCTTTGATGATCCCTCCAATG
TCAACGTGCAGAACCTAGACAAGGCCCGGCAAGCAGGGGGTGGTGCTGGGAGCCCCAATCCTGCCATCAATGGCAGCACA
CCCTGAGACCTGTTTGACATGAAGCCCTTTGAAGATGCTCTTCACATGCCTCCTCCTCCCCAGTTGGTGTCCATGGTTAA
GCAGCTCTGAGGGGACCCTGGTTCCATGGGAAGCTGAGTTAGCAGGAGGCTGAGGCACTGCTGCAGCTCAACGGGGACTT
CCTGGTGCAGGAGAGCATGACCACACCTGGCCAGTATGTGCTCACTGGCTTGCAGAGTGGGGAGTCCAAGCATCTGCTAC
TGGTGGACCCTGAGGGTGTAGTTCGGACAAAGGATCACCGCTTTGAGAGTGTCAGTCACCTCATCAGCTACCACATGGAC
AATCACTTGCCCATCACCTCTGCTGGCAGTGAACTGTGTCTACAGCAACCTGTGGAGCAGAAACTG

Alignment

ORF - retro_ptro_3117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDLLPPKPKYNPLRNESLSSLEEGASGSTPPEELPSPSASSLGPILPPLPGDDSPTTLCSFFPRMSNLRL
          M.LLPPK.K.NPL.NESLSSLEEG.SGSTPPEELPSPSASSLGPILPPLPG..SPTTLCSFFP.MSNLRL
Retrocopy MNLLPPKSKCNPLWNESLSSLEEGPSGSTPPEELPSPSASSLGPILPPLPGNHSPTTLCSFFPWMSNLRL

Parental  ANPAGGRPGSKGEPGRAADDGEGIVGAAMPDSGP-LPLLQDMNKLSGGGGRRTRVEGGQLGGEEWTRHGS
          AN.AGG..G.KGEPGRAA.DGEGIVGA.MPDS.P.LPLLQDMNKLSGGGG.RT.VEGGQLGGEEWTR.GS
Retrocopy ANWAGGHLGPKGEPGRAANDGEGIVGATMPDSFP<LPLLQDMNKLSGGGGCRTQVEGGQLGGEEWTRRGS

Parental  FVNKPTRGWLHPNDKVMGPGVSYLVRYMGCVEVLQSMRALDFNTRTQVTREAISLVCEAVPGAKGATRRR
          FVNKP..G.LHPNDKV..PGVSYL..YMGCVE.LQSM.ALDFNT.TQVTREAISLVCEAVPGAKG.TRRR
Retrocopy FVNKPMWG*LHPNDKVTRPGVSYLIWYMGCVEILQSMSALDFNTWTQVTREAISLVCEAVPGAKGVTRRR

Parental  KPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAK
          KPC..PLSSILGRSNLKFA.M.ITLT.STSSLN.M.ADCKQII.NHHMQSISF.S.GDPDTA.YVA.VAK
Retrocopy KPCNHPLSSILGRSNLKFAAMTITLTISTSSLNVMVADCKQIITNHHMQSISFTSSGDPDTAKYVANVAK

Parental  DPVNQRACHILECPEGLAQDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQY
          DPV.Q.ACHILECPEGLAQDVISTIGQAF.L.FKQYLR.PPKLVTPHDRM.GF.G.AWDEEEEEPP.HQ.
Retrocopy DPVSQKACHILECPEGLAQDVISTIGQAFKLHFKQYLRKPPKLVTPHDRMTGFHGLAWDEEEEEPPGHQH

Parental  YNDF-PGKEPPLGGVVDMRLREGAAPGAARPTAPNAQTPSHLGATLPVGQPVGGDPEVRKQMPPPPPCPA
          YNDF.PGKE.PL..VV.MRLREGA.PGAARPT.P.AQTPSHLG.TLPVGQ.VGGDPEV.K.MPPPPPCP.
Retrocopy YNDF<PGKESPLWHVVYMRLREGATPGAARPTPPSAQTPSHLGSTLPVGQSVGGDPEVCK*MPPPPPCP-

Parental  GRELFDDPSYVNVQNLDKARQAVGGAGPPNPAVNGSVPRDLFDMKPFEDALRVPPPPQSVSMAEQLRGE-
          GRELFDDPS.VNVQNLDKARQA.GGAG.PNPA.NGS.P.DLFDMKPFEDAL..PPPPQ.VSM..QL.G..
Retrocopy GRELFDDPSNVNVQNLDKARQAGGGAGSPNPAINGSTP*DLFDMKPFEDALHMPPPPQLVSMVKQL*GD<

Parental  PWFHGKLSRREAEALLQLNGDFLVRESTTTPGQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLI
          PWFHGKLS..EAEALLQLNGDFLV.ES.TTPGQYVLTGLQSG..KHLLLVDPEGVVRTKDHRFESVSHLI
Retrocopy PWFHGKLS*QEAEALLQLNGDFLVQESMTTPGQYVLTGLQSGESKHLLLVDPEGVVRTKDHRFESVSHLI

Parental  SYHMDNHLPIISAGSELCLQQPVERKL
          SYHMDNHLPI.SAGSELCLQQPVE.KL
Retrocopy SYHMDNHLPITSAGSELCLQQPVEQKL

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	20.20 RPM
SRP007412_cerebellum	0.00 RPM	21.08 RPM
SRP007412_heart	0.03 RPM	28.74 RPM
SRP007412_kidney	0.00 RPM	65.61 RPM
SRP007412_liver	0.07 RPM	75.98 RPM
SRP007412_testis	0.00 RPM	14.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3117 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3117 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4690
Pongo abelii	retro_pabe_3643

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009236	1 retrocopy	retro_cjac_2573,
Homo sapiens	ENSG00000160691	1 retrocopy	retro_hsap_4690,
Nomascus leucogenys	ENSNLEG00000011515	1 retrocopy	retro_nleu_2362,
Pongo abelii	ENSPPYG00000000769	1 retrocopy	retro_pabe_3643,
Pan troglodytes	ENSPTRG00000001397	1 retrocopy	retro_ptro_3117 ,
Tarsius syrichta	ENSTSYG00000011380	1 retrocopy	retro_tsyr_1773,