RetrogeneDB ID: retro_ogar_1934

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873575.1:10418040..10418936(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000005478
• Aliases: None
• Description: None

Sequence

>retro_ogar_1934
GTGACTGCAACAAGGGAGAACACAGCTTACACTGTGGAATGTCTGAGGGGTGATGTTGATATTCTAATAGAATTCCTGCT
TCGTGTCACCAACAGCACCAGAATGTTGTGTTGGGAAGTAGCGGACCTTCAGTGTTAACTAAGGACTGACAAAGCTATAG
TTTTTCAGATTCCACAGGCTCAAGTCATTGAAAATTTGCATGCTGCAGCTCACCAAATGCCTTGGCTTATTCCCTATATT
GTCCTGACTATAGGATTGGAAAAGTGACATCAGAGGAGTTACATTACCATGTTCAGAACCATTTTACAAGTGCAAGAATG
GCTTTAGTTGGACTTGGTGTGAGTAATCCTGTGCTTAAGCACATTGCTGAACAGTTTCTCAACATAATGGGAGGGGTTGG
TTTAACTGGTGCTAAGGCCAGATACCCTGGAAGTGAAATTCCAGAGCAGAAGGGAAACAGCTTGTCCACGCTGCTCTTGT
AACAGAAAGTGCTGCCACAGGAAGTGCAAAAGCAAATGCATTTAGTCTTCTTCAGCATGTGCTTGGTGCTGGACCTCCTT
GTCAAGAGGGGCAGCAATGCCACCAGCCTTCTATACCAGGCTGTTGCCAAGGGAATTCACCAGCCATTTGACATTTCTGC
TTTTAATGCCAGTTACTCAGATTCTGGACTTTTCAGGATTTATATAATCTCCCAGGCTGCAGCTGCTGGAGATGTTATCA
AGTCTGCCTATAACCAGATCAAAACAATTGCTCAAGGAAACCTTTCCAATGCAGATGTCCAAGCTGCCGGAAACAAGCTG
AAAGCTGGATGCCTAATGTCAGTGGAGTCTTCTGAGGGTTTCCTGGATGAAGTTGGATCCCAGGAACTAGCTACTGGTTT
TTACGGGCCACCATCC

Alignment

ORF - retro_ogar_1934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 66. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTATRENIAYTVECLRGDVDILMEFLLNVTTAPEFRRWEVADLQSQLRVDKAVAFQNPQAQVIENLHAAA
          VTATREN.AYTVECLRGDVDIL.EFLL.VT.......WEVADLQ..LR.DKA..FQ.PQAQVIENLHAAA
Retrocopy VTATRENTAYTVECLRGDVDILIEFLLRVTNSTRMLCWEVADLQC*LRTDKAIVFQIPQAQVIENLHAAA

Parental  YR-NALANSLYCPDYRIGKVTAEELHYYVQNHFTSARMALVGLGVSHPVLKQIAEQFLNMRGGLGLTGAK
          ...NALA.SLYCPDYRIGKVT.EELHY.VQNHFTSARMALVGLGVS.PVLK.IAEQFLN..GG.GLTGAK
Retrocopy HQ<NALAYSLYCPDYRIGKVTSEELHYHVQNHFTSARMALVGLGVSNPVLKHIAEQFLNIMGGVGLTGAK

Parental  ARYRGGEIREQNGNSL-VHAALVAEGAASGSAEANAFSLLQHVLGAGPH-VKRGSNTTSLLYQAVAKGVH
          ARY.G.EI.EQ.GNSL.VHAALV.E.AA.GSA.ANAFSLLQHVLGAGP..VKRGSN.TSLLYQAVAKG.H
Retrocopy ARYPGSEIPEQKGNSL<VHAALVTESAATGSAKANAFSLLQHVLGAGPP>VKRGSNATSLLYQAVAKGIH

Parental  QPFDVSAFNASYSDSGLFGIYTISQAASAGDVIKAAYNQIKTIAQGSLSKADVQAARNKLKAGYLMSVES
          QPFD.SAFNASYSDSGLF.IY.ISQAA.AGDVIK.AYNQIKTIAQG.LS.ADVQAA.NKLKAG.LMSVES
Retrocopy QPFDISAFNASYSDSGLFRIYIISQAAAAGDVIKSAYNQIKTIAQGNLSNADVQAAGNKLKAGCLMSVES

Parental  SEGFLDEVGSQALVAGSYIPPS
          SEGFLDEVGSQ.L..G.Y.PPS
Retrocopy SEGFLDEVGSQELATGFYGPPS

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_1934 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934 , retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,