RetrogeneDB ID: retro_ogar_397

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:60282748..60283451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCMF1
• Ensembl ID: ENSOGAG00000034863
• Aliases: None
• Description: potassium channel modulatory factor 1 [Source:HGNC Symbol;Acc:20589]

Sequence

>retro_ogar_397
GTGATTTGTCCAATATGTACTGCGTTCCCTGGAGGCGATCCTGATCACGTCACAGATGACTTTACAGCTCATCTTACACT
TGAACGCAGAGCCCCTAGAGATTTAGAATATAGTGGTGTTTGACGCCTATGTAGAATGTTTCACCCTGGCTAAGGATTAG
GAGGCCCTCATGCTTGTAGATCAAAAGTACACTGTACTAGCGGTTCTACTGGTGGACGTTCTTCTGCTCAGAGTTCATAT
TTCCCAACCCATAGGGAAGCCATGGATCCTATAGCTGAGCTTTTATCTCAGTTATTGAAAGCGAGACGTTCTGCAGGAGG
ACAGCTTAATCCTTCTGGCCCTTTGGCTTCTCAGTTAGATAACTGCAGATGCAGGGCAGCTAGAATGGCAGCATCTGGAG
ACGGCATGCGACACAACCCGGCACACTAACATAAGCAGTGTCACCAGTATGATCACACAATCCACAGCAACAGCCAACAC
AGCTAATACAGAAAGCTGTCAGCAGACTCTCTAGAATGCCCTGTTTCTTTTAACAAGGTTGAATGATCTTCAGTGTCTGA
AACAGAGTGCCAGTCCATGGAAAGTGAGTGTGCAGACCACAGCCTGTTTCTCCATGAGCTCCTTCTGTCACTTTAGTGAG
CAAAGAGAGCTCGTCCTAAGAGGAAGGCGAATGGGGGAGACGGCACATTTGACTGCTATGGGC

Alignment

ORF - retro_ogar_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.53 %
• Parental protein coverage: 65.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VICPICAALPGGDPNHVTDDFAAHLTLEHRAPRDLIYDESSGVRHVRRMFHPGRGLGGPRARRSNMHFTS
          VICPIC.A.PGGDP.HVTDDF.AHLTLE.RAPRDL.Y...SGV....RMFHPG.GLGGP.A.RS..H.TS
Retrocopy VICPICTAFPGGDPDHVTDDFTAHLTLERRAPRDLEY---SGV*RLCRMFHPG*GLGGPHACRSKVHCTS

Parental  SSTGGLSSSQSSYSPSNREAMDPIAELLSQLSGVRRSAGGQLNSSGPSASQLQQ-LQMQ-LQLERQHAQA
          .STGG.SS.QSSY.P..REAMDPIAELLSQL...RRSAGGQLN.SGP.ASQL...LQMQ..QLE.QH...
Retrocopy GSTGGRSSAQSSYFPTHREAMDPIAELLSQLLKARRSAGGQLNPSGPLASQLDN<LQMQ<GQLEWQHLET

Parental  ARQQLETARNATRRTNTSSVTTTITQSTATTNTANTESSQQTLQNSQFLLTRLND-PKMSETERQSMESE
          A.....T.R.......TS..T....QSTAT.NTANTES.QQTL.N..FLLTRLND....SETE.QSMESE
Retrocopy A---CDTTRHTNISSVTSMIT----QSTATANTANTESCQQTL*NALFLLTRLND<SSVSETECQSMESE

Parental  RADRSLFVQELLLS-TLVREESSSSDEDE-RGEMADFGAMG
          .AD.SLF..ELLLS.TLV..ESSS..E.E..GE.A...AMG
Retrocopy CADHSLFLHELLLS<TLVSKESSS*EEGE<MGETAHLTAMG

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_397 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005786	1 retrocopy	retro_chof_1282,
Dasypus novemcinctus	ENSDNOG00000006752	2 retrocopies	retro_dnov_1000, retro_dnov_2063,
Echinops telfairi	ENSETEG00000001809	1 retrocopy	retro_etel_1685,
Myotis lucifugus	ENSMLUG00000000979	1 retrocopy	retro_mluc_1781,
Monodelphis domestica	ENSMODG00000015567	1 retrocopy	retro_mdom_1682,
Otolemur garnettii	ENSOGAG00000034863	2 retrocopies	retro_ogar_3140, retro_ogar_397 ,
Vicugna pacos	ENSVPAG00000010386	1 retrocopy	retro_vpac_650,