RetrogeneDB ID: retro_ptro_165

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:79439943..79441548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSPTRG00000006587
• Aliases: SNW1, SKIIP
• Description: None

Sequence

>retro_ptro_165
ATAGCGTTGCCAGATAAAACACCTGCACCTACTCAGTTATCTCAGGACCAGCTTGAGGCTGAAGAAAAGACAAGATCCCA
GAGATCATGGCAGACTTCGTTTGTCTCTTCCGGAAGAGAACCTTCCCCGTAAGGATACCGGAAAGGCTGGACACTTCGGT
TATTAGAGGATTTTGGAGATGGAGGTGCTTTTCCAGAAATCCATGTGGCTCAGTATCCACTGGATATGGGACGAAAGAAA
AAAATATCTAGTGCGCTGGCCATTCAGGTGGATTCTGAAGGAAAAATCAAATATGATGGAATCACTCGACAAGGACAGTC
AAAAGACAAGGTCATTTATAGCAAATACACTGTCCTGGTTCCAAAGGATGTTATGAATGCAAATGATCCAGACTTGCAAA
GGCCCGATGAAGAAGCTATAAAAGAGATAACAGAAAAGACAAGAGTAGCCTTATAAAAAGCTGTACCACAGAAGGTCACC
GCAGTCACGCCAGTTCAGGCAGCTGACAAACCGGCTCCTGCTCAGTATATCCGATACACACCATCTCAGCAAGGAGTGGC
TTTCAACTCTGGAGTTAAACAGAGGGTTAGTCGGATGGTAGAAGTGCAGAAAGATCCAACGGAGCCTCCAAGGTTCAAGA
TTAATAAGAAAATTCCCCGGGGACCACCTTCTCCTCCTATGCCTGTCATGCATTCTCCCAGCCGAAAGATGATTGTAAGG
GAACAACAGGAGTATAAGTTTCCTCCTTGTATTTCTAACTGGAAAAATGCAAAGGGTTATACAATTCCATTAGACAAACG
TCTGGCTGCCGAAGGAAGAGGACTACAGACAGTACACATAAAAGAAAATGTTGCCACATTGGTGATCCTCTACATTGCTG
ATCAGAAGGCTTGTGAAGCTGTGGGAATGCGTGCCCGAGTAGAGAGAAAAATGGCTCAGAAAGAAAAGGGAAAATATGAA
GAGAAGCTTAGAGAAATGGCACAGAAAGCCAGGGAGAGAAGAGCTGGGATCAAAACTCATGTGGAAAAAGAGGATAGGGA
GGCACGTGAGAGGAATGAAATCCGGCATGACAGGCGCAAAGAGAGACAGCATGACCAGAATCTTTCCAGGGCAGCTCCTG
ATAAGAGGTCGAAACTGCAGAGAAATGAAAATGGGGATATCAGTGAAGTCATTGCTGTCGGTGTTCCTAATCCTTGAACT
TCCAATGAAGGTCAGTACGACCAAAGGCTCGTCAACCAATCCAAGGGTATGGACAGTGGATTTGCAGGTGGAGAAGATGG
AATTTATAATGTTTATGATCAAGCCTAGAGAGGTGGTAAAGATATGGCCCACAGTAGTTATAGGCCCAGTAAAAATCTGG
ACAAGGACATGTATGACGATGACCTAGAAGCCAGAATAAACACCAACAGATTTGTTCCTGACAAAGAGTTTTCTGGTTCA
GGCTGTAAGCAGAGAGGCCGAGAAGGACCAGTTCAGTTTGAGGAAGATCCTTTTGGTTTGGACAAGTTTTTGGAAGAAGT
GAAACAGCACGGTGGCTCTAAAAGACCCTCAGATAGCAGCCACCCCATGGAATATGAGCATGAAGGCAAGAAGGGGAGGA
AGGAC

Alignment

ORF - retro_ptro_165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
          .AL....PAPTQLSQDQLEAEEK.RSQRS.QTS.VSS.REP.P.GYRKGW..RLLEDFGDGGAFPEIHVA
Retrocopy IALPDKTPAPTQLSQDQLEAEEKTRSQRSWQTSFVSSGREPSP*GYRKGWTLRLLEDFGDGGAFPEIHVA

Parental  QYPLDMGRKKKMSNALAIQVDSEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAI
          QYPLDMGRKKK.S.ALAIQVDSEGKIKYD.I.RQGQSKDKVIYSKYT.LVPK.VMNA.DPDLQRPDEEAI
Retrocopy QYPLDMGRKKKISSALAIQVDSEGKIKYDGITRQGQSKDKVIYSKYTVLVPKDVMNANDPDLQRPDEEAI

Parental  KEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPP
          KEITEKTRVAL.K.V.QKV.A..PV.AADK.APAQYIRYTPSQQGVAFNSG.KQRV.RMVE.QKDP.EPP
Retrocopy KEITEKTRVAL*KAVPQKVTAVTPVQAADKPAPAQYIRYTPSQQGVAFNSGVKQRVSRMVEVQKDPTEPP

Parental  RFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHI
          RFKINKKIPRGPPSPP.PVMHSPSRKM.V.EQQE.K.PPCISNWKNAKGYTIPLDKRLAA.GRGLQTVHI
Retrocopy RFKINKKIPRGPPSPPMPVMHSPSRKMIVREQQEYKFPPCISNWKNAKGYTIPLDKRLAAEGRGLQTVHI

Parental  NENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEAR
          .EN.A.L...LYIAD.KA.EAV.MRA.VERKMAQKEK.K.EEKLREMAQKARERRAGIKTHVEKED.EAR
Retrocopy KENVATLV-ILYIADQKACEAVGMRARVERKMAQKEKGKYEEKLREMAQKARERRAGIKTHVEKEDREAR

Parental  ERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDS
          ER.EIRHDRRKERQHD.NLSRAAPDKRSKLQRNEN.DISEVIA.GVPNP.TSNE.QYDQRL.NQSKGMDS
Retrocopy ERNEIRHDRRKERQHDQNLSRAAPDKRSKLQRNENGDISEVIAVGVPNP*TSNEGQYDQRLVNQSKGMDS

Parental  GFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREG
          GFAGGED.IYNVYDQA.RGGKDMA.S.YRPSKNLDKDMY.DDLEARI.TNRFVPDKEFSGS...QRGREG
Retrocopy GFAGGEDGIYNVYDQA*RGGKDMAHSSYRPSKNLDKDMYDDDLEARINTNRFVPDKEFSGSGCKQRGREG

Parental  PVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
          PVQFEEDPFGLDKFLEE.KQHGGSKRPSDSS.P.E.EHEGKK.RK.
Retrocopy PVQFEEDPFGLDKFLEEVKQHGGSKRPSDSSHPMEYEHEGKKGRKD

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	28.90 RPM
SRP007412_cerebellum	0.04 RPM	52.23 RPM
SRP007412_heart	0.06 RPM	38.74 RPM
SRP007412_kidney	0.00 RPM	34.23 RPM
SRP007412_liver	0.00 RPM	35.45 RPM
SRP007412_testis	0.00 RPM	206.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_165 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_165 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_174
Gorilla gorilla	retro_ggor_257
Pongo abelii	retro_pabe_454
Callithrix jacchus	retro_cjac_2932

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165 ,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,