RetrogeneDB ID: retro_pabe_454

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:150326462..150327479(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSPPYG00000006031
• Aliases: SNW1, SKIIP
• Description: SNW domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001127521]

Sequence

>retro_pabe_454
ATAGCGTTGCCAGATAAAACACCTGCACCTACTCAGTTATCTCAGGACCAGCTTGAGGCTGAAGAAAAGACAAGATCCCA
GAGATCACGGCAGACTTCATGTGTCTCTTCCGGAAGAGAACCTTCCCCGTACGGATACCGGAAAGGCTGGACACTTCGGT
TATTAGAGGATTTTGGAGATGGAGGTGCTTTTCCAGAAATCCATGTGGCTCAGTATCCACTGGATATGGGACGAAAGAAA
AAAATGTCTAATGTGCTGGCCATTCGGGTGGATTCTGAAGGAAAAATTAAATATGATGGAATCACTCTACAAGGACAGTC
AAAAGACAAGGTAATTTATAGGAAATACACTGTCCTGGTTCCAAAGGATGTTATGAATGCAAATGATCCAGACTTGCAAA
GGCCCGATGAAGAAGCTATAAAAGAGACAACAGAAAAGACAAGAGTAGCCTTATAAAAAGCTGTAACACAGAAGGTCGCC
GCAGTCACGCCAGTTCAGGCAGCTGACAAACCGGCTCCTGCTCAGTATATCCGATACACACCATCTCAGCAAGGAGTGGC
TTTCAACTCTGGAGCTAAACAGAGGGTTAGTCGGATGGTAGAAGTGCAGAAAGATCCAACGGAGCCTCCAAAGTTCAAGA
TTAATAAGAAAATTCCCCGGGGACCACCTTCTCCTCCTGTACCTGTCATGCATTCTCCTAGCCAAAAGATGATTGTAAGG
GAACAACAAGAGTGAAAGTTTCCTCCTTGTATTTCTAACTGGAAAAATGCAAAGGGTTACACAATTCCATTAGACAGATG
TCTGGCTGCCGATGGAAGAGGACTACAGACAGTACACATAAAAGAAAATGTTGCCACATTGGCCGAAGCCCTCTACATTG
CTGATCAGAAGGCTTGTGAAGCTGTGGAAATGCGTGCCCGAGTAGAGAGAAAAATGGCTCAGAAAGAAAAGGGAAAATAT
GAAGAGAAACTTAGAGAAATGGCCCAGAAAGCCAGGGATAGAAGAGCTGGGATCAAA

Alignment

ORF - retro_pabe_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.86 %
• Parental protein coverage: 63.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
          .AL....PAPTQLSQDQLEAEEK.RSQRSRQTS.VSS.REP.PYGYRKGW..RLLEDFGDGGAFPEIHVA
Retrocopy IALPDKTPAPTQLSQDQLEAEEKTRSQRSRQTSCVSSGREPSPYGYRKGWTLRLLEDFGDGGAFPEIHVA

Parental  QYPLDMGRKKKMSNALAIQVDSEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAI
          QYPLDMGRKKKMSN.LAI.VDSEGKIKYD.I..QGQSKDKVIY.KYT.LVPK.VMNA.DPDLQRPDEEAI
Retrocopy QYPLDMGRKKKMSNVLAIRVDSEGKIKYDGITLQGQSKDKVIYRKYTVLVPKDVMNANDPDLQRPDEEAI

Parental  KEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYXXXXKLAPAHGVNSGAKQRVIRMVEMQKDPMEPP
          KE.TEKTRVAL.K.V.QKVAA..PV.AADK.APAQY............NSGAKQRV.RMVE.QKDP.EPP
Retrocopy KETTEKTRVAL*KAVTQKVAAVTPVQAADKPAPAQYIRYTPSQQGVAFNSGAKQRVSRMVEVQKDPTEPP

Parental  RFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHI
          .FKINKKIPRGPPSPP.PVMHSPS.KM.V.EQQE.K.PPCISNWKNAKGYTIPLD..LAADGRGLQTVHI
Retrocopy KFKINKKIPRGPPSPPVPVMHSPSQKMIVREQQE*KFPPCISNWKNAKGYTIPLDRCLAADGRGLQTVHI

Parental  NENFAKLAEALYIADRKVGQAVTARSLLGINLTKEVKDRHKENDKRLMKVTEEEAGHVK
          .EN.A.LAEALYIAD.K...AV..R...........K....E................K
Retrocopy KENVATLAEALYIADQKACEAVEMRARVERKMAQKEKGKYEEKLREMAQKARDRRAGIK

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	2.93 RPM	19.46 RPM
SRP007412_cerebellum	3.89 RPM	14.84 RPM
SRP007412_heart	1.72 RPM	10.60 RPM
SRP007412_kidney	2.75 RPM	15.65 RPM
SRP007412_liver	2.11 RPM	12.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_454 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_454 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_174
Pan troglodytes	retro_ptro_165
Gorilla gorilla	retro_ggor_257
Callithrix jacchus	retro_cjac_2932

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 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,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
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,