RetrogeneDB ID: retro_nleu_982

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:11615904..11617490(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSNLEG00000016771
• Aliases: None
• Description: None

Sequence

>retro_nleu_982
CCTGCACCTACTCAGTTATCTCAGGACCAGCTCGAGGCTGAAGAAAAGACAAGATCCCAGAGATCATGGCAGACTTCATT
TGTCTCTTCCGGAAAAGAACCTTCCCCGTACGGATACCGGAAAGGCTGGACACTTCGGTTATTAGAGGATTTTGGAGATG
GAGGTGCTTTTCCAGAGATCCATGTGGCTCAGTATCCACTGGATATGGGACGAAAGAAAAAAATATCTAATGAGCTGGCC
ATTAAGGTGGATTCTGAAGGAAAAATTAAATATGACGTAATCACTCGACAAGGACAGTCAAAAGACAAGGTGATTGATAG
CAAATACACTGTCCTGGTTCCAGAAGATGTTATGAATGCAAATGATCCAGACTCGCAAAGGCCTGATGAAGAAGCTATAA
AAGAGATAACAGAAAAGACAAGAGCAGCCTTATAAAAAGCTGTACCACAGAACGTCGCCGTAGTCATGCCAGTTCAGGCA
GCTGACAAACCAGCTCCTGCTCAGCATATCTGATACACACCATCTCGGCAAGCAGTGACTTTCAACTCTGGAGCTCAACA
GAAGGTTAGTCGGATGGTAGAAGTGCAGAAAGATCCAACGGAGCCTCTAAGGTTCAAGATTAATAAGAAAATTCCCCGGG
GACCACCTTCTCCTCCTGTACCTGTCATGCATTCTCCTAGCCGAAAGATGATTGCAAGGGAACAACAAGAGTGAAAGTTT
CCTCCTTGTATTTCTAACTGGAAAAATGCAAAGGTTATGCAATTCCATTAGACAAACGTCTGGCTGCCGATGGAAGAGGA
CTACAAACAGTACACATAAAAGAAAATGTTGCCACGTTGGCCGAAGCCCTCTACATTGCTGATCAGAAGGCTTGTGAAGC
TGTGGAAATGCGTCCCCGAGTAGAAAGAAAAATGGCTCAGAAAGAAAAGGGAAAATATGAAGAGAAGCTTAGAGAAATGG
CCCAGAAAGCCAAGGATAGAAGAGCTGGGATCAAAACTCATGTGGACAGAAAGGATAGGGAGGCACGTGAGAGGAATGAA
ATATGGCATGACAGGCGAAAAGAGAGACAGCATGACCAGAATCTTTCCAGGGCAGCTCCTGATAAGAGGTCGAAACTTCA
GAGAAATGAAAATGGGGGTATCAGTGAAGTCATTGCCCTCGGTGTTCCTAATCCTTGAACTTCCAACGAAGGTCAGTACG
ACCAAAGGCTCCTCAACCAATCCAAGGGTATGGACAGTGGATTTGCAGGTGGAGAAGATGAAATTTATAATGTTTATGAT
CAAGCCTAGAGAGGTGGTAAAGATATGGCCCATAGTATTTATAGGCCCAGTAAAAATCTGGACAAGGACATGTATGACGA
TGACCTAGAAGCCAGAATAAAGATCAACAGATCTGTTCCCGACAATGAGTTTTCTGGTTCAGGCTGTAAGCAGAGAGGCC
GAGAAGGACCAGTTCAGTTTGAGGAAGATCCTTTTGGTTTGGGCAAGTTTTTGGAAGAAGCGAAACAGCACGGTGGCTCT
AAAAGACCCTCAGATAGCAGCTGCCTCATGGAATATGAGCATGAAGGCAAGAAGAGGAGGAAGGAC

Alignment

ORF - retro_nleu_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVAQYPLDMG
          PAPTQLSQDQLEAEEK.RSQRS.QTS.VSS..EP.PYGYRKGW..RLLEDFGDGGAFPEIHVAQYPLDMG
Retrocopy PAPTQLSQDQLEAEEKTRSQRSWQTSFVSSGKEPSPYGYRKGWTLRLLEDFGDGGAFPEIHVAQYPLDMG

Parental  RKKKMSNALAIQVDSEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAIKEITEKT
          RKKK.SN.LAI.VDSEGKIKYD.I.RQGQSKDKVI.SKYT.LVP..VMNA.DPD.QRPDEEAIKEITEKT
Retrocopy RKKKISNELAIKVDSEGKIKYDVITRQGQSKDKVIDSKYTVLVPEDVMNANDPDSQRPDEEAIKEITEKT

Parental  RVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKINKK
          R.AL.K.V.Q.VA..MPV.AADK.APAQ.I.YTPS.Q.V.FNSGA.Q.V.RMVE.QKDP.EP.RFKINKK
Retrocopy RAAL*KAVPQNVAVVMPVQAADKPAPAQHI*YTPSRQAVTFNSGAQQKVSRMVEVQKDPTEPLRFKINKK

Parental  IPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAK-GYTIPLDKRLAADGRGLQTVHINENFAK
          IPRGPPSPP.PVMHSPSRKM...EQQE.K.PPCISNWKNAK.GY.IPLDKRLAADGRGLQTVHI.EN.A.
Retrocopy IPRGPPSPPVPVMHSPSRKMIAREQQE*KFPPCISNWKNAK<GYAIPLDKRLAADGRGLQTVHIKENVAT

Parental  LAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDEIR
          LAEALYIAD.KA.EAVEMR..VERKMAQKEK.K.EEKLREMAQKA..RRAGIKTHV...D.EARER.EI.
Retrocopy LAEALYIADQKACEAVEMRPRVERKMAQKEKGKYEEKLREMAQKAKDRRAGIKTHVDRKDREARERNEIW

Parental  HDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDSGFAGGE
          HDRRKERQHD.NLSRAAPDKRSKLQRNEN..ISEVIALGVPNP.TSNE.QYDQRL.NQSKGMDSGFAGGE
Retrocopy HDRRKERQHDQNLSRAAPDKRSKLQRNENGGISEVIALGVPNP*TSNEGQYDQRLLNQSKGMDSGFAGGE

Parental  DEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREGPVQFEE
          DEIYNVYDQA.RGGKDMA.SIYRPSKNLDKDMY.DDLEARIK.NR.VPD.EFSGS...QRGREGPVQFEE
Retrocopy DEIYNVYDQA*RGGKDMAHSIYRPSKNLDKDMYDDDLEARIKINRSVPDNEFSGSGCKQRGREGPVQFEE

Parental  DPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
          DPFGL.KFLEEAKQHGGSKRPSDSS...E.EHEGKKRRK.
Retrocopy DPFGLGKFLEEAKQHGGSKRPSDSSCLMEYEHEGKKRRKD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_982 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,