RetrogeneDB ID: retro_ogar_2820

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873667.1:1422708..1423188(-)
• Located in intron of: ENSOGAG00000002544

Retrocopy information

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

Parental gene information

• Parental gene symbol: LITAF
• Ensembl ID: ENSOGAG00000028239
• Aliases: None
• Description: lipopolysaccharide-induced TNF factor [Source:HGNC Symbol;Acc:16841]

Sequence

>retro_ogar_2820
ATGTGGGTTTTAGGCATTTACGAGGCAGCCACCAGGCCTTCCTCAGTGCTGTCTGTGCCCCAACCTGGGAAGAGACGGAG
GCTGTTAACAATGACTACCGCAGGCCTCTAGCATCTGTGCCTGGGCCCACTACGGGGCTCATGACGGCCCAGATCGGAGG
GCACGAATCCTGCTTCATATTGTCCCCAGCCAGTGCCTGTCCCCAGGGCCAGTGCAATTGCCATGTGGGTGGCCTGTGTG
CAAGAACCTGTCCCCTCTTTTGACCACCCTGTTCAGATATGTTGTCCTTCCTGCAACAAGGTGATCGTGGCTCAGCTGTC
CTGTAATACCATTGCTCTGACCTGGCTGTCCTGGGGAGGCCTGTGCCTGCTGGGGCACATAGCAGGCTGCTGCTTCACCG
TTTTCTGCATGGACACCCTGCAGGACACGGACTGCTATTGTCCCGACTGCTAAGCTCTTCCGGGCATCTCCAAGCATTTG

Alignment

ORF - retro_ogar_2820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSVPGPYQAAAGPSSAPTAP-PSYEETVAVNNYYPTPPAPMPGPTTGLMT-GPD-GKGMNPPSYYTQPVP
          M.V.G.Y.AA..PSS....P.P..EET.AVNN.Y..P.A..PGPTTGLMT.GPD...G.NP.SY..QPVP
Retrocopy MWVLGIYEAATRPSSVLSVP<PTWEETEAVNNDYRRPLASVPGPTTGLMT<GPD<SEGTNPASYCPQPVP

Parental  VPNANAIAVQTVYLQQPVSFFDHPVQMCCPSCNKMIVTQLSYNAGALTWLSCGSLCLLGCIAGCCFIPFC
          VP.A.AIA......Q.PV..FDHPVQ.CCPSCNK.IV.QLS.N..ALTWLS.G.LCLLG.IAGCCF..FC
Retrocopy VPRASAIAMWVACVQEPVPSFDHPVQICCPSCNKVIVAQLSCNTIALTWLSWGGLCLLGHIAGCCFTVFC

Parental  VDALQDVDHYCPNCKALLGTYKRL
          .D.LQD.D.YCP.C.AL.G..K.L
Retrocopy MDTLQDTDCYCPDC*ALPGISKHL

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_2820 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820 ,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,