RetrogeneDB ID: retro_pabe_3643

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:61771927..61773670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHC1
• Ensembl ID: ENSPPYG00000000769
• Aliases: None
• Description: SHC-transforming protein 1 [Source:RefSeq peptide;Acc:NP_001126253]

Sequence

>retro_pabe_3643
ATGAATCTCCTGCCCCCCAAGTCCAAGTACAATCCACTGTGGAATGAGTCTCTGTCATCGCCGGAGGAGGGGCCTTCAGG
GTCCACCCCACCAGAGGAGCTGCCTTCCCCATCAGCCTCATCCCTGGGGCCCATCCTGCCCCCTCTGCCTGGGAACCATA
GTCCCACTACCCTGTGCTCCTTCTTCCCCTGGATGAGCAACCTGAGGCTGGCCAATTGGGCCGGGGGACACCTGGGGCCT
AAGGGGGAGCCAGGAAGGGCAGCCAATGATGGGGAGGGCATCGTAGGGGCAACTATGCCCGACTCATTCCCCTACCCCTC
CTCCAGGACATGAACAAGCTGAGTGGATGTGGTGGGTGCAGGACTCAGGTGGAAGGGGGCCAGCTTGGGGGCAAGGAGTG
GACCCACCATGGGAGCTTTGTCAGTAAGCCCATGTGGGGCTGGCTGCATCCCAATGACAAAGTCATGAGACCTGGGGTTT
CCTACTTGGTTTGGTACATGGGCTGTGTGGAGGTCCTGCAGTCAATGAGTGCTCTGGACTTCAACACCTGGACTCAGATC
ACCAGGGAGGCCATCAGTCTTGTATGTGAGGCTGTGCCAGGTGCCAAGCGGGCGACAAGGAGGAGAAAGCCCTGTAGCCA
TCCACTCAGCTCTATCCTGGGAAGGAGTAACCTGAAATTTGCTGGAATGACAATCACTCTCACCATCTCCACCAGCAGCC
TCAACGTCATGGTTGCAGACTGCAAACAGATTATCACTAACCACCATATGCAATCTATCTCTGCATTCAGTGGGGATCTG
GACATAGCCAAGTATGTCACCAACGTTGCCAAAGACCCTGTGAGTCAGAAAGCCTGCCACGTTCTGGAGTGTCCTGAAGG
GCTTCCCAGGATGTCATCAGCACCATTGGCCAGGCCTTCGAGTTGCACTTTAAACAATACCTCAGGAAACCACCCAAACT
GGTCACCCCCCATGACAAGATGACTGGCTTTGATGGCTTAGCTTGGGATGAGGAGGAGGAAGAGCCACCTGGCCATCAGC
ACTATAATGACTTCCTGGGAAGGAACCCCCTCTTTGGCGTGTGGTATACATGAGGCTTCAGGAAGGAGCCACTCCAGGGG
CTGTTCGACCCACTCTACCCAGTGCCCAGACCCCCAGCCACTTGGGAGCTACACTGTCTGTAGAACAGTCTGTTGGGGGA
GATCCAGAAGTCTGCAAATAGATGCCACCTCTACCACCCTGTCCAGGCAGAGAGCTCTTTGATGATCCCTCCAATGTCAA
CGTGCAGAACCTAGACAAGGCCTGGCAAGCAGGAGGTGGTGCTGGGACCCCCAATCCTGCCATCAATGGCAGCACACCCT
GGGACCTGTTTGACATGAAGCCCTTTGAAGATGCTTTTCACATGCCTCCTCCTCCCCAGTTGGTGTCCATGGCTGAGCAG
CTCTGAGGGGACCCCTGGTTCCATGGGAAGCTGAGCTAGCGGGAGGCTGAGGCACAGCTGCAGCTCAACGGGGACTTCCT
GGTGCAGGAGAGCATGACCACACCTGGCCAGTATGTGCTCACTGGCTTGCAGAGTGGGGAGCCCAAGCATCTGCTACTGG
TGGACCCTGAGGGTGTAGTTTGGACAAAGGATCACTGCTTTGAGAGTGTCAGTCACCTCATCAGCTACCACATGGACAAT
CACTTGCCCATCATCTCTGTGGGCAGTGAACTGTGTCTACAGCAATCTATGGAGCAGAAACTG

Alignment

ORF - retro_pabe_3643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDLLPPKPKYNPLRNESLSSLEEGASGSTPPEELPSPSASSLGPILPPLPGDDSPTTLCSFFPRMSNLRL
          M.LLPPK.KYNPL.NESLSS.EEG.SGSTPPEELPSPSASSLGPILPPLPG..SPTTLCSFFP.MSNLRL
Retrocopy MNLLPPKSKYNPLWNESLSSPEEGPSGSTPPEELPSPSASSLGPILPPLPGNHSPTTLCSFFPWMSNLRL

Parental  ANPAGGRPGSKGEPGRAADDGEGIVGAAMPDSGP-LPLLQDMNKLSGGGGRRTRVEGGQLGGEEWTRHGS
          AN.AGG..G.KGEPGRAA.DGEGIVGA.MPDS.P.LPLLQDMNKLSG.GG.RT.VEGGQLGG.EWT.HGS
Retrocopy ANWAGGHLGPKGEPGRAANDGEGIVGATMPDSFP<LPLLQDMNKLSGCGGCRTQVEGGQLGGKEWTHHGS

Parental  FVNKPTRGWLHPNDKVMGPGVSYLVRYMGCVEVLQSMRALDFNTRTQVTREAISLVCEAVPGAKGATRRR
          FV.KP..GWLHPNDKVM.PGVSYLV.YMGCVEVLQSM.ALDFNT.TQ.TREAISLVCEAVPGAK.ATRRR
Retrocopy FVSKPMWGWLHPNDKVMRPGVSYLVWYMGCVEVLQSMSALDFNTWTQITREAISLVCEAVPGAKRATRRR

Parental  KPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAK
          KPCS.PLSSILGRSNLKFAGM.ITLT.STSSLN.M.ADCKQII.NHHMQSIS.A..GD.D.A.YV..VAK
Retrocopy KPCSHPLSSILGRSNLKFAGMTITLTISTSSLNVMVADCKQIITNHHMQSIS-AFSGDLDIAKYVTNVAK

Parental  DPVNQRACHILECPEGL-AQDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQ
          DPV.Q.ACH.LECPEGL..QDVISTIGQAFEL.FKQYLR.PPKLVTPHD.M.GFDG.AWDEEEEEPP.HQ
Retrocopy DPVSQKACHVLECPEGL<SQDVISTIGQAFELHFKQYLRKPPKLVTPHDKMTGFDGLAWDEEEEEPPGHQ

Parental  YYNDF-PGKEPPLGGVVDMRLREGAAPGAARSTAPSAQTPSHLGATLPVGQPVGGDPEVRKQMPPPPPCP
          .YNDF.PGKEPPL..VV.MRL.EGA.PGA.R.T.PSAQTPSHLGATL.V.Q.VGGDPEV.K.MPP.PPCP
Retrocopy HYNDF<PGKEPPLWRVVYMRLQEGATPGAVRPTLPSAQTPSHLGATLSVEQSVGGDPEVCK*MPPLPPCP

Parental  AGRELFDDPSYVNVQNLDKARQAVGGAGPPNPAVNGSAPRDLFDMKPFEDALRVPPPPQSVSMAEQLRGE
          .GRELFDDPS.VNVQNLDKA.QA.GGAG.PNPA.NGS.P.DLFDMKPFEDA...PPPPQ.VSMAEQL.G.
Retrocopy -GRELFDDPSNVNVQNLDKAWQAGGGAGTPNPAINGSTPWDLFDMKPFEDAFHMPPPPQLVSMAEQL*GD

Parental  PWFHGKLSRREAEALLQLNGDFLVRESTTTPGQYVLTGLQSGGPKHLLLVDPEG-VRTKDHRFESVSHLI
          PWFHGKLS.REAEA.LQLNGDFLV.ES.TTPGQYVLTGLQSG.PKHLLLVDPEG.V.TKDH.FESVSHLI
Retrocopy PWFHGKLS*REAEAQLQLNGDFLVQESMTTPGQYVLTGLQSGEPKHLLLVDPEGVVWTKDHCFESVSHLI

Parental  SYHMDNHLPIISAGSELCLQQPVERKL
          SYHMDNHLPIIS.GSELCLQQ..E.KL
Retrocopy SYHMDNHLPIISVGSELCLQQSMEQKL

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	0.39 RPM	47.72 RPM
SRP007412_cerebellum	0.00 RPM	28.33 RPM
SRP007412_heart	0.18 RPM	24.93 RPM
SRP007412_kidney	0.70 RPM	65.73 RPM
SRP007412_liver	0.67 RPM	62.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3643 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3643 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4690
Pan troglodytes	retro_ptro_3117

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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,