RetrogeneDB ID: retro_ggor_257

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:81039095..81040679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSGGOG00000026016
• Aliases: None
• Description: None

Sequence

>retro_ggor_257
CCTGCACCTACTCAGTTATCTCAGGACCAGCTTGAGGCTGAAGAAAAGACAAGATCCCAGAGATCATGGCAGACTTCATT
TGTCTCTTCCGGAAGAGAACCTTCCCCGTAAGGATACCGGAAAGGCTGGACATTTCGGTTATTAGAGGATTTTGGAGATG
GAGGTGCTTTTCCAGAAATCCATGTGGCTCAGTATCCACTGGATATGGGACGAAAGAAAAAAATATCTAGTGCGCTGGCC
GTTCAGGTGGATTCTGAAGGAAAAATCAAATATGATGGAATCACTCGACAAGGACAGTCAAAAGACAAGGTCATTTATAG
CAAATACACTGTCCTGGTTCCAAAGGATGTTACGAATGCAAATGATCCAGACTTGCAAAGGCCCGATGAAGAAGCTATAA
AAGAGATAACAGAAAAGACAAGAGTAGCCTTATAAAAAGCTGTACCACAGAAGGTCACCGCAGTCACGCCAGTTCAGGCA
GCTGACAAACCGGCTCCTGCTCAGTATATCCGATACACACCATCTCAGCAAGGAGTGGCTTTCAACTCTGGAGTTAAACA
GAGGGTTAGTCGGATGGTAGAAGTGCGGAAAGATCCAACGGAGCCTCCAAGGTTCAAGATTAATAAGAAAATTCCCCGGG
GACCACCTTCTCCTCCTGTGCCTGGCATGCGTTCTCCTAGCCGAAAGATGATTGTAAGGGAACAACAAGAGTAAAAGTTT
CCTCCTTGTATTTCTAACTGGAAAAATGCAAAGGGTTATACAATTCCATTAGACAAACGTCTGACTGCCGAAGGAAGAGG
ACTACAGACAGTACACATAAAAGAAAATGTTGCCACATTGGTGATCCTCTACATTGCTGATCAGAAGGCTTGTGAAGCTG
TGGAAATGCGTGCCCGAGTAGAGAGAAAAATGGCTCAGAAAGAAAAGGGAAAATATGAAGAGAAACTTAGAGAAATGGCA
CAGAAAGCCAGGGAGAGAAGAGCTGGGATCAAAACTCATGTGGAAAAAGAGGATAGGGAGGCACGTGAGAGGAATGAAAT
CCAGCATGACAGGCGAAAAGAGAGACAGCATGACCAGAATCTTTCCAGGGCAGCTCCTGATAAGAGGTCGAAACTGCAGA
GAAATGAAAATGGGGATATCAGTGAAGTCATTGCTCTCGGTGTTCCTAATCCTTGAACTTCCAATGAAGGTCAGTACGAC
CAAAGGCTCGTCAACCAATCCAAGGGTATGGACAGTGGATTTGCAGGTGGAGAAGATGGAATTTATAATGTTTATGATCA
AGCCTAGAGAGGTGGTAAAGATATGGCCCACAGTAGTTATAGGCCCAGTAAAAATCTGGACAAGGACATGTATGACGATG
ACCTAGAAGCCAGAATAAAGACCAACAGATTTGTTCCCGACAAAGAGTTTTCTGGTTCAGGCTGTAAGCAGAGAGGCCGA
GAAGGACCAGTTCAGTTTGAGGAAGATCCTTTTGGTTTGGACAAGTTTTTGGAAGAAGTGAAACAGCACGGTGGCTCTAA
AAGACCCTCAGATAGCAGCCGCCCCATGGAATATGAGCATGAAGGCAAGAAGAGGAGGAAGGAC

Alignment

ORF - retro_ggor_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.73 %
• Parental protein coverage: 98.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVAQYPLDMG
          PAPTQLSQDQLEAEEK.RSQRS.QTS.VSS.REP.P.GYRKGW..RLLEDFGDGGAFPEIHVAQYPLDMG
Retrocopy PAPTQLSQDQLEAEEKTRSQRSWQTSFVSSGREPSP*GYRKGWTFRLLEDFGDGGAFPEIHVAQYPLDMG

Parental  RKKKMSNALAIQVDSEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAIKEITEKT
          RKKK.S.ALA.QVDSEGKIKYD.I.RQGQSKDKVIYSKYT.LVPK.V.NA.DPDLQRPDEEAIKEITEKT
Retrocopy RKKKISSALAVQVDSEGKIKYDGITRQGQSKDKVIYSKYTVLVPKDVTNANDPDLQRPDEEAIKEITEKT

Parental  RVALEKSVSQKVAAAMPVRAADKLAPAQYIRNPLSNHYKCIVFNNNSKPVYCLCRQLKAEFFKVSTFRIN
          RVAL.K.V.QKV.A..PV.AADK.APAQYIR...S.......FN...K..................F.IN
Retrocopy RVAL*KAVPQKVTAVTPVQAADKPAPAQYIRYTPSQ--QGVAFNSGVKQRVSRMVEVRKDPTEPPRFKIN

Parental  KKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENFA
          KKIPRGPPSPP.P.M.SPSRKM.V.EQQE.K.PPCISNWKNAKGYTIPLDKRL.A.GRGLQTVHI.EN.A
Retrocopy KKIPRGPPSPPVPGMRSPSRKMIVREQQE*KFPPCISNWKNAKGYTIPLDKRLTAEGRGLQTVHIKENVA

Parental  KLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDEI
          .L...LYIAD.KA.EAVEMRA.VERKMAQKEK.K.EEKLREMAQKARERRAGIKTHVEKED.EARER.EI
Retrocopy TLV-ILYIADQKACEAVEMRARVERKMAQKEKGKYEEKLREMAQKARERRAGIKTHVEKEDREARERNEI

Parental  RHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDSGFAGG
          .HDRRKERQHD.NLSRAAPDKRSKLQRNEN.DISEVIALGVPNP.TSNE.QYDQRL.NQSKGMDSGFAGG
Retrocopy QHDRRKERQHDQNLSRAAPDKRSKLQRNENGDISEVIALGVPNP*TSNEGQYDQRLVNQSKGMDSGFAGG

Parental  EDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREGPVQFE
          ED.IYNVYDQA.RGGKDMA.S.YRPSKNLDKDMY.DDLEARIKTNRFVPDKEFSGS...QRGREGPVQFE
Retrocopy EDGIYNVYDQA*RGGKDMAHSSYRPSKNLDKDMYDDDLEARIKTNRFVPDKEFSGSGCKQRGREGPVQFE

Parental  EDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
          EDPFGLDKFLEE.KQHGGSKRPSDSSRP.E.EHEGKKRRK.
Retrocopy EDPFGLDKFLEEVKQHGGSKRPSDSSRPMEYEHEGKKRRKD

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	1.44 RPM	34.43 RPM
SRP007412_cerebellum	1.10 RPM	33.13 RPM
SRP007412_heart	0.31 RPM	12.20 RPM
SRP007412_kidney	0.90 RPM	30.26 RPM
SRP007412_liver	0.87 RPM	20.21 RPM
SRP007412_testis	2.07 RPM	96.24 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_257 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_174
Pan troglodytes	retro_ptro_165
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,