RetrogeneDB ID: retro_ogar_2049

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873585.1:1034716..1035192(+)
• Located in intron of: ENSOGAG00000014338

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSOGAG00000010975
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_ogar_2049
ACAGGCTGTGGGTCCTATGCCGTACGTGCTTACAAACCTGTGTCCCCACCTAATACCCGGGTAATTCTCATCCTTGGGCC
TGGTCATCACTTGTCCTTCTCTCAATGTGCACTTTCTGGTGTAGACATATATAGGTCAGCTCTGTATGACCTTTCTATTG
GCCAAAGATTTACAGAAAACTATCGAAGACGGGAATGTTTGAACACATGTCTCTGCAGACAGATGAAGATGCACAAGTGT
TGAAATGCATTTGCCTTATATGGCTAAACCATGGAAAGCCATAGCATGGGTTTGCCATTATTCCTGTACTGGTTGGGGCT
CTGAGTGAATCAAAAGAATAGAAATTTGGAAAATTCTTCAGTAAATGTCTAGCATTTTCTACTAATCTCTTTGTGCTCTC
TTCTGATTTCTGCCCCTGGGGTCAAAGTTTTCATTAGAATTATTATGATGGATCCCAGGGCGAGATTTATAGATCA

Alignment

ORF - retro_ogar_2049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.9 %
• Parental protein coverage: 57.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TYCGSCAAHAYKQVDPSITRRIFILGPSHHVPLSRCALSSVDIYRTPLYDLRIDQ-KIYGELWKTGMFER
          T.CGS.A..AYK.V.P..TR.I.ILGP.HH...S.CALS.VDIYR..LYDL.I.Q.KIY..L.KTGMFE.
Retrocopy TGCGSYAVRAYKPVSPPNTRVILILGPGHHLSFSQCALSGVDIYRSALYDLSIGQ<KIYRKLSKTGMFEH

Parental  MSLQTDEDEH-SIEMHLPYTAK-AMESHK-DEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSS
          MSLQTDED...S.EMHLPY.AK..MESH....F.IIPVLVGALSESKE..FGK.FSK.LA...NLFV.SS
Retrocopy MSLQTDEDAQ<SVEMHLPYMAK<TMESHS<HGFAIIPVLVGALSESKE*KFGKFFSKCLAFSTNLFVLSS

Parental  DFCHWGQRFRYSYYDESQGEIYRS
          DFC.WGQ.F...YYD.SQGEIYRS
Retrocopy DFCPWGQSFH*NYYDGSQGEIYRS

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_2049 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049 , retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,