RetrogeneDB ID: retro_ogar_2827

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873668.1:2165393..2166064(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSOGAG00000004869
• Aliases: None
• Description: tetraspanin 6 [Source:HGNC Symbol;Acc:11858]

Sequence

>retro_ogar_2827
GTGGTCCTGATTTACACTTCAGTCTTTTAGATCACTGTTGTTGCCTTCCTTGCCATTGGCATTTGGAGCAAGGTGAGCCT
GGAGAATTATTTTTCCCTTTTAAATGAGAAGGCCACCAATATCCCCTTCATGGTCATTGGCACTGGCACTGTCATTATTC
TTTTGGGTACCTTTGGTTGTTTTGCTGCCTGCCAAGCTTCTGCATGGATGCTAAAATTGCAGGTCATATTTCTGACTCTC
ATTCTTTTGGTTGAACTGGTCACTGCCATTGTAGGATTTGTATTCAGATATGAGATTATCATCAGCTCTAAGAATAATCA
TGAGAAGGCTTTGAAGCAATATAACTCTATGGGAGACTAAAGAAGCGTTGCAATAGACAAGATCCAAAATACACTGCATT
GTTGTAGTGTCACCAGTTATAGAGATTGCACAGATACTAATTATTATTCAGAAAAAGAATTTTCCAAGAGTTGCTATAAA
CTTGAAAATTATTCTCTGCAGAGAGATACAGGTAAACAATGAGGTTGTTTTACAAAGATGATAACCATTATAGAGTCAGA
AATGGGAGTCATTGCCGGAAGTTCCTTTGGAGTCTCTCGCTTCCAATTGATGGGAATCTTTCTAGCCCACTGCCTCTTTC
CTGCCAAATAAATAACCAGTATGTGACAGTG

Alignment

ORF - retro_ogar_2827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.25 %
• Parental protein coverage: 79.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLLIYTFIFWITGVVLLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGTVIILLGTFGCFATCRASAWM
          V.LIYT..F.IT.V..LA.GIW.KVSLENYFSLLNEKATN.PF..IGTGTVIILLGTFGCFA.C.ASAWM
Retrocopy VVLIYTSVF*ITVVAFLAIGIWSKVSLENYFSLLNEKATNIPFMVIGTGTVIILLGTFGCFAACQASAWM

Parental  LKLYAMFLTLIFLVELVAAIVGFVFRHEIKNSFKNNYVKALKQYNSTGDYKSDAVDKIQNTLHCCGVTDY
          LKL...FLTLI.LVELV.AIVGFVFR.EI..S.KNN..KALKQYNS.GD..S.A.DKIQNTLHCC.VT.Y
Retrocopy LKLQVIFLTLILLVELVTAIVGFVFRYEIIISSKNNHEKALKQYNSMGD*RSVAIDKIQNTLHCCSVTSY

Parental  RDWTDTNYYSEKGFPKSCCKHEDCSPQRDADKVNNEGCFLKVMTIIESKMGVVAGISFGVACFQLIGIFL
          RD.TDTNYYSEK.F.KSC.K.E..S.QRD..K....GCF.K..TIIES.MGV.AG.SFGV..FQL.GIFL
Retrocopy RDCTDTNYYSEKEFSKSCYKLENYSLQRDTGK--Q*GCFTKMITIIESEMGVIAGSSFGVSRFQLMGIFL

Parental  AYCLSRA-ITNNQYEIV
          A.CL..A...NNQY..V
Retrocopy AHCLFPA<QINNQYVTV

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_2827 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827 ,
Otolemur garnettii	ENSOGAG00000008547	2 retrocopies	retro_ogar_1615, retro_ogar_3124,
Otolemur garnettii	ENSOGAG00000016713	2 retrocopies	retro_ogar_2407, retro_ogar_469,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,