RetrogeneDB ID: retro_ogar_1404

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873545.1:4282149..4282981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSOGAG00000029825
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_ogar_1404
GCTAAACAAAGGGTTATTCACATGGTAGAAATGCATGAAGACCCAATGGAGCCTCCAAAGTTCAAGATCAATAAGAAAAT
TCCCCGGGGACCACCTTCTCCTTCTGCACCTGTCATGCATTCTCCTAGCAGAAAGATGACTGTAAAGGAACAACCAGAGT
GGAAGGTTCCTCCTTGTATCTATAACTGGAAAAATGCAAAGGGTTATACAATTCCATTAGACAAATGTCTAGCTGCTGAT
GGATGAGGACTACAGACAGTACACCTAAATGAAAATTTTGCCAGACTGGCTGAAGCTCTTTATAGTTCTGATTGGAAGAC
TCGTGAAGCTGTGGAAATGCACACCCAAGTAGGAGAAAAATGGCTCAGAAAGAAAAGGGGAAACACAAAGAGAAACTTAG
AGAAATGGCTCAGAAAGCCAGAGAAAGGCAAGCTGGGACCAAAACCCATATGGAGAAAGAGGATGGCGAGGCACATGAGA
GGGATGAAATCCCACACTATAGGTGAAAAGAGAGACAGCATGACAGGAATCTTTCCAGGGGAGCGCCTGATAAGAGGTCA
AATCTGTAGAGAAATGAAAATTGGGATATCAGTGAAGTCATTGCTCTTGGTGTGCCCCATCCTTGGACTTCCAATGAAGT
TCAGGATGACCAAAGGCTCTTCAACCAATCCAAGGGCATGGACAGTGGGTTTGCAAATGAAGAAGATGAAATTTATAATG
ATCAAGACTGGAGAGGTAAGATATGGCCCAGAGCATTTATAGTTCTGGTAAAAATCTGGACAAGGACATGTATGGTGATG
ACCTAGAAGCCAGAATAAAGACCAACAGATTT

Alignment

ORF - retro_ogar_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 52.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKQRVIRMVEMQKDPMEPPRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYT
          AKQRVI.MVEM..DPMEPP.FKINKKIPRGPPSP.APVMHSPSRKMTVKEQ.EWK.PPCI.NWKNAKGYT
Retrocopy AKQRVIHMVEMHEDPMEPPKFKINKKIPRGPPSPSAPVMHSPSRKMTVKEQPEWKVPPCIYNWKNAKGYT

Parental  IPLDKRLAADGRGLQTVHINENFAKLAEALYIADRKAREAVEMRAQV-ERKMAQKEKEKHEEKLREMAQK
          IPLDK.LAADG.GLQTVH.NENFA.LAEALY..D.K.REAVEM..QV..RKMAQKEK.KH.EKLREMAQK
Retrocopy IPLDKCLAADG*GLQTVHLNENFARLAEALYSSDWKTREAVEMHTQV<RRKMAQKEKGKHKEKLREMAQK

Parental  ARERRAGIKTHVEKEDGEARERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPR
          ARER.AG.KTH.EKEDGEA.ERDEI.H.R.KERQHDRNLSR.APDKRS.L.RNEN.DISEVIALGVP.P.
Retrocopy ARERQAGTKTHMEKEDGEAHERDEIPHYR*KERQHDRNLSRGAPDKRSNL*RNENWDISEVIALGVPHPW

Parental  TSNEVQYDQRLFNQSKGMDSGFAGGEDEIYNVYDQAWRGGK-DMAQSIYRPSKNLDKDMYGDDLEAKLKT
          TSNEVQ.DQRLFNQSKGMDSGFA..EDEIYN..DQ.WR.GK.DMAQSIY...KNLDKDMYGDDLEA..KT
Retrocopy TSNEVQDDQRLFNQSKGMDSGFANEEDEIYN--DQDWR-GK<DMAQSIYSSGKNLDKDMYGDDLEARIKT

Parental  NRF
          NRF
Retrocopy NRF

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1404 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 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,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
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,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404 ,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,