RetrogeneDB ID: retro_ogar_3285

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873765.1:1642956..1643797(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000034143
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTAP
• Ensembl ID: ENSOGAG00000007889
• Aliases: None
• Description: methylthioadenosine phosphorylase [Source:HGNC Symbol;Acc:7413]

Sequence

>retro_ogar_3285
ATGGCCTCAAGCGCTGCCACCACTGCAGTGAAGATTGGAATAATTGGTGGAACAGGCCTGGATGATCCAGAAATTTTAGG
AGGAAGAACTGAAAAATATGTGGATACTCCATTTGGCAAACCCTCTGATGCCTTAAATGGGGGGAAGATAAAAAATGTCG
ATTGTGTTCTCCTTGCAAGGCCTGGGAGGCAGCGCACCATCATTCCTTCAGAAATCAACTACCAGGCACACATCTGGCCT
TTGAAGGCAGAAGGACATGTCATAGTGACGGCAGCTTGTGGCTCCTTGGGGGAGGAGATTCAGCCTGGGGATATAGTCAT
TATTGATCAGTTCATGGACAGGACCATCATGAGGCCACCACCTTCTATGATGGAAGTCATTCCTATACCAGGGGAGTGTG
CCACATGCCCATGGCTGAGCCGTTTGGCCCCGAAACAAGAGAGGTCCTCATCGAGACTGCTCAGAAGTGTGGACTCCAGT
GCCACTCAAAGGGGACAATGGGGACAATGGGAGGACCTCATTTTAGCTCCCGGGCAGAAACCCTTGTGTTCCACACCTGG
GGGCAGATATTGTCAACACGACCACAGTCCCAGAAGTGGTTCTTGCAAAGGAGGTTGGAATCTGCTATACGAGTATCGCC
ATGGCAACAGATTACCATTGCTGGAAGGAGCCCCAGGAAGCATTTTCTGTGGCCTGGATCTTAGAGACCCTGAAAGAAAA
CTCCAGTAAGGCCCCAAGTTTACTTCTCACCACCGTTCCTCAGACAGGGTCCACGGAATGGTCAGAAACTCTCCATAACC
TGGAGAATACGGCCCAGTTTTCTGTTTTATTGCTGAGACAT

Alignment

ORF - retro_ogar_3285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAQRTTRTAATIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCVLLARHGRQHTIMPS
          .A.....TA..IGIIGGTGLDDPEIL.GRTEKYVDTPFGKPSDAL..GKIKNVDCVLLAR.GRQ.TI.PS
Retrocopy MASSAATTAVKIGIIGGTGLDDPEILGGRTEKYVDTPFGKPSDALNGGKIKNVDCVLLARPGRQRTIIPS

Parental  KINYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTTMRPQ-TFYDGNHSCTRGVCHIP
          .INYQA.IW.LK.EG..HVIVT.ACGSL.EEIQPGDIVIIDQF.DRT.MRP..TFYDG.HS.TRGVCH.P
Retrocopy EINYQAHIWPLKAEG--HVIVTAACGSLGEEIQPGDIVIIDQFMDRTIMRPP<TFYDGSHSYTRGVCHMP

Parental  MAEPFCPKTREVLIETAKKLGLRCHSKGTMVTIEGPRFSSRAESLVFRTWG-ADVINMTTVPEVVLAKEA
          MAEPF.P.TREVLIETA.K.GL.CH.........GP.FSSRAE.LVF.TWG.AD..N.TTVPEVVLAKE.
Retrocopy MAEPFGPETREVLIETAQKCGLQCHXXXXXXXXXGPHFSSRAETLVFHTWG<ADIVNTTTVPEVVLAKEV

Parental  GICYASIAMATDYDCWKEHEEVVSVDRVLKTLKENANKAKSLLLTTIPQIGSMEWSETLHDLKNMAQFSV
          GICY.SIAMATDY.CWKE..E..SV...L.TLKEN..KA.SLLLTT.PQ.GS.EWSETLH.L.N.AQFSV
Retrocopy GICYTSIAMATDYHCWKEPQEAFSVAWILETLKENSSKAPSLLLTTVPQTGSTEWSETLHNLENTAQFSV

Parental  LLPRH
          LL.RH
Retrocopy LLLRH

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_3285 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285 ,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,