RetrogeneDB ID: retro_ogar_2133

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873594.1:6211691..6212494(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM106B
• Ensembl ID: ENSOGAG00000009729
• Aliases: None
• Description: transmembrane protein 106B [Source:HGNC Symbol;Acc:22407]

Sequence

>retro_ogar_2133
ATGGGACAGTCTCTTTCTCTTTTGCCTTTGCATTCAAGTAAAGAATATGCTTATGATGGAGTCACACCCCCTAACAGTAT
GAGGAATGGATTGGTTAACAGTAAAGTCCAGAAGGAAGATGAAGAAGCACAGATGTCTCTGAGTTCCCATGTGTGGAATT
TATGGGAAAAGAAAGTGTCACTTGCCCACTTGTCAGGGAACAGGAAGAATTCCCAGGGGGCCAGAAAACCAACTGATGGC
ATTGATTCCATACAGTGGTCAGAGGTTAAGGCCAGGAATATCAGGCTGTACGTGACGGCTTCTGCTCATCCATCTGCTCC
TTTGGGATCAGCTATGTTTTTCCTTTTCCCTCTCCCATGACTTGAAATATATTGGTGTAAAATGAGCATGTGTCAGTTAC
AGTGTTCAAAAGCGTATGATATATTTAAGTATTATAAACACACTAAGTACTAAGAACAGTAATCATCATTCTGTCAAAGT
TGAAAATATCACTGTTTAGGTTCAGTTTTCCAAAACAGTTGCTAGGAAAAACACACTTAAACATCACCAGTATTGGTCCA
TGGGATATGAGACAAAGTGATTACACAGTACCTACTATTATAGCAGAGGATACGAATCACCTGCTTGATTTCTGTACATT
GACATCCATTAAAGTACATAACAGTATTAATGATACAAGGGACTGTGACAACAACATACTGTGGCCACTCTGAGCAGATA
TGCCAGGAGAGGTACCAGCCTATAGCTGTGGAAGGAACATGACTTATCAGTTGGAATCTCTAAATGTGCGTCGGCCATAC
CAG

Alignment

ORF - retro_ogar_2133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MGKSLSHLPLHSSKEDAYDGVTSSDNMRNGLVSGEVHNEDG-RNGDVSQFPYVEFTGRDSVTCP-TCQGT
          MG.SLS.LPLHSSKE.AYDGVT....MRNGLV...V..ED..R..DVS.FP.VEF.G..SVTCP.TCQGT
Retrocopy MGQSLSLLPLHSSKEYAYDGVTPPNSMRNGLVNSKVQKEDE<RSTDVSEFPCVEFMGKESVTCP<TCQGT

Parental  GRIPRDLGQENQLVALIPYSDQRLRP-RRTKLYVMASVFVCLLLSGLAVFFL-FPR-SIDVKYIGVKSAY
          GRIPR..G.ENQL.ALIPYS.QRLRP.R...LYV.AS......L.G.A.FFL.FP..S.D.KYIGVK.A.
Retrocopy GRIPR--GPENQLMALIPYSGQRLRP<RNIRLYVTASAHPSAPL-GSAMFFL<FPS<SHDLKYIGVK*AC

Parental  VSYDPQKRRIYLNITNTLNITNNNYYSVEVENITAQVQFSKTV-IGKARLNNITNIGPLDMKQIDYTVPT
          VSY..QKR.IYL.I.NTL...N.N..SV.VENIT..VQFSKTV..GK..L.NIT.IGP.DM.Q.DYTVPT
Retrocopy VSYSVQKRMIYLSIINTLSTKNSNHHSVKVENITV*VQFSKTV>LGKTHL-NITSIGPWDMRQSDYTVPT

Parental  VIAEEMSYMFDFCTLVSIKVHN-IVVMMQVTVTTTYFGHSEQTSQERYQYV-DCGRNTTYQLGQSEYLNV
          .IAE......DFCTL.SIKVHN..........T.TY.GHSEQ..QERYQ....CGRN.TYQL...E.LNV
Retrocopy IIAEDTNHLLDFCTLTSIKVHN>VLMIQGTVTT-TYCGHSEQICQERYQPI<SCGRNMTYQL---ESLNV

Parental  LQPQQ
          ..P.Q
Retrocopy RRPYQ

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_2133 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002306	1 retrocopy	retro_cfam_50,
Mustela putorius furo	ENSMPUG00000014079	1 retrocopy	retro_mputfur_72,
Otolemur garnettii	ENSOGAG00000009729	1 retrocopy	retro_ogar_2133 ,