RetrogeneDB ID: retro_ogar_1238

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873540.1:8494943..8495784(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030293
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000000273
• Aliases: None
• Description: None

Sequence

>retro_ogar_1238
GTACTGAACAGGCTGGATATGCTGCTTGCCCAGAAGGATCGGCTCAGGAGGCGGAACTTGCAAGTGCTGGATTTGTAGGA
TATCAAGGGAAACTTCTGGACAGTATGGTGTGGAGACCCAGCACGCTCCTCAGAAGCCACAAAGAAGAGACCAACAGCAA
AGGACTGTGTGGGGATGAGAAGGCCAGGGCCGGTGATGGTCTTCGTAGACTTGGCCTTGACAGAAAGCACCCTGGATCAG
TGCCTCACCTACCTTCCTCGCTGGGTTAGGAAGAGAAAAGATGCTCTCCACCTGTGCTGTAGGAAGCTGATGATAGAGGA
GATGATGGGCCAGAATATGAGGAAGGTCCTAGAAATGGTGGACCTGGACTGTATCCAGAAGGTGCAACTAAACTGTGGCT
CTGACCTGTCCACCACTGCGGGCTTTGCTCCTTAACTGGGCCAGATGAGTAATCTCAGCAAACTGGATCTCTTAAACGTC
TATGAATGTGGCATAATTCCCCAAATCAGAATGGCGAGATTGTTGCCTAGTTCACCTCTCAGCTCCTCAAGTTAAACCAC
CTTGGAAGCTTCATGTGTATGTTTGCTTTCTGAGACACGGTCTTCAGCAGGTTCTCAGGTGCAGGTGCTTTAAAGCCCCT
TTGAAAATCTTCTTACTTTATTTCTGTAACCTATCCACATCAGACTGGGAGAACCTGTCCCCTTGGCCAAGCATGAGTTA
GCCAAAGGAGTTGCATCTGGAAGACATTGAACTGACCCATTTCAGTCCCGAGCCTCTTAAACTTTTGCTAGAGAAGGGTG
CAGGCACCGTCCAGTCCTTGGTTCTAGAGGATGGTGGACTC

Alignment

ORF - retro_ogar_1238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.75 %
• Parental protein coverage: 59.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLDGLDALLAQKVRPRRWNLQVLELGDVDGDFRSVWYGGAECSSEAMKKRRTTNDSAGTGRQRPVVVSAD
          VL..LD.LLAQK.R.RR.NLQVL.L.D..G.F..VW.G....SSEA.KKR.T..D..G..R..PV.V..D
Retrocopy VLNRLDMLLAQKDRLRRRNLQVLDL*DIKGNFWTVWCGDPARSSEATKKRPTAKDCVGMRRPGPVMVFVD

Parental  LSLTEGNLDPCLTYLVQWVRNRKDALHLCCRKLVISEIAFLNVSEVLEVVDLDCVREVEVDCSPELSPEP
          L.LTE..LD.CLTYL..WVR.RKDALHLCCRKL.I.E....N...VLE.VDLDC...V...C...LS...
Retrocopy LALTESTLDQCLTYLPRWVRKRKDALHLCCRKLMIEEMMGQNMRKVLEMVDLDCIQKVQLNCGSDLSTTA

Parental  VFAPYLGQMSNLGKLVLCNIFVCPL-SSPKEKEQIVARFTSQLFKLHNLR-ELAVYTGSFLVFCLHQVL-
          .FAP.LGQMSNL.KL.L.N...C....SP.....IVA.FTSQL.KL..L...L.VY...FL...L.QVL.
Retrocopy GFAP*LGQMSNLSKLDLLNVYECGI<NSPNQNGEIVA*FTSQLLKLNHLG<KLHVYV-CFLRHGLQQVLR

Parental  -RCLETPLETFLMTKCLLSTSDWENLSSWPSISQLKELRLGGIILAHLSPEPLSLLLEKIAATVQSLFLE
          .RC...PL..FL...C.LSTSDWENLS.WPS.S..KEL.L..I.L.H.SPEPL.LLLEK.A.TVQSL.LE
Retrocopy CRCFKAPLKIFLLYFCNLSTSDWENLSPWPSMS*PKELHLEDIELTHFSPEPLKLLLEKGAGTVQSLVLE

Parental  NCGI
          ..G.
Retrocopy DGGL

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_1238 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013324	1 retrocopy	retro_dord_231,
Homo sapiens	ENSG00000187545	1 retrocopy	retro_hsap_220,
Mus musculus	ENSMUSG00000025839	1 retrocopy	retro_mmus_557,
Otolemur garnettii	ENSOGAG00000000273	2 retrocopies	retro_ogar_1100, retro_ogar_1238 ,
Ochotona princeps	ENSOPRG00000009716	1 retrocopy	retro_opri_661,
Pan troglodytes	ENSPTRG00000029629	1 retrocopy	retro_ptro_330,
Rattus norvegicus	ENSRNOG00000042820	1 retrocopy	retro_rnor_1371,
Rattus norvegicus	ENSRNOG00000048835	1 retrocopy	retro_rnor_396,