RetrogeneDB ID: retro_ogar_1100

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873535.1:23054014..23055339(-)
• Located in intron of: ENSOGAG00000010051

Retrocopy information

• Ensembl ID: ENSOGAG00000028904
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ogar_1100
CAGGGTGCACCAAGACTCTTGGACCTGGCTGTGCAAAGCATGGTGAGTAATGAAGTCTTGGCCATATCTGCTCTGGAGGA
GCTGCCCAGGGAGCTCTTCCCACCGCTGTTCGTGGAGGCCTTCACCAGGAGATGCAGCAGAGTCTGACAGCGATGGTGCA
GGCCTGGCCCTTCCTGCGCCTCCCTCTGGGGGTCCCTGATAACACGTGACCTGGAGGTGTTAAAAGCTGTGCTGGACAGG
CTGGATGCGCTCCTTGCCCAGAAGGTTCCGCCCAGGAGGTGGAACCTTCAAGTGCTGGATTTGCAGGATATCAAGGGAAA
CTTCTGGACAGTATGGTGTGGAGACCCAGAGTGCTCCTCAGAAGCCACAGAGCAGAGACCAACAGCAAAGGACTGCAGGG
ATGCGAAGGCTACGGCCCATCATGGTGTCCATAGAATTGACCTTGACAGAAAGCACCCTGGATCAGTGGCTTATCTATCT
CCTTTGGTGGGTTAGGAAGAAAAAAGATGCTTTCCACCTGTGCTGTAGGAAGCTGCTGATAGAGGAGATGATGGGCCAGA
ATATGAGGAAGGTGCTGGAAATGGTGGACCTGGACTGTATCCAGGAGGTGAAACTAGACTGTGGCTCTGACCTGTCCACC
ACCATGGGCTTTGCTCCTTATCTGGGCCAGATGAGTAGTCGCAGCAAACTGGATCTCTTAAACAGCTATGAACTTGGCAA
CAATTCCCCAAATCAGAACGAGATTATCTCCCAGGTCACCTCTCAGCTCCTAAAGTTAAACAACCTCCGGAAGCTTCATA
TGTATCTTTGCTTCCTGAGACACAGTCTTCAGTAGGTGCTTGGGTGCTTTGAAGCCCCTTTGGAAACCCTCTTCCTTAAT
TACTGTAACCTATCTGCATCAGACTGGGAGAACCTGTCCTCTTGGCCGAGCATGAGTCAGCTAAAGGAGTTACATCTGGA
AGACATTGCATTGACCCATTTCAGTCCCGAGCCCCTTAAACTTTTCCTAGAGAATGTTGCAGGCACAGGCCAGTCCTTGG
TTCTAGAGGACTGTGGGATGGTAGACTCCCAACTCAATGTCATCATGCCTGCCCTGAGCTGCTGCTGCCAGCTCACAACC
CGTGGGAACTTCTTCTCCTGGGCCACCCTGGAGCACCTGCTGCACCACACTGCCAGGCTGAGCAAGTTAAGCCTGGAGGT
CTACTCTGCCCCTCTGGAGAGTTATGATGCCCAGGAAAGTTCTGGATTCCAGGAAGTATTACCAATTTCAGGCTGAGCTG
ACAGAGATACTGAGGGGCATAAGGAAGCCCAAGAAGATTGCGTTC

Alignment

ORF - retro_ogar_1100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 95.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTPPSLLDLAVQSLVRNEALAISALEELPGLLFPPLFLEAFTRRHRRV-LTAMVQAWPFTRLPLG-SLMK
          Q..P.LLDLAVQS.V.NE.LAISALEELP..LFPPLF.EAFTRR..RV.LTAMVQAWPF.RLPLG.SL..
Retrocopy QGAPRLLDLAVQSMVSNEVLAISALEELPRELFPPLFVEAFTRRCSRV<LTAMVQAWPFLRLPLG>SLI-

Parental  TGDLKTLKAVLDGLDALLAQKVRPRRWNLQVLELGDVDGDFRSVWYGGAECSSEAMKKRRTT-NDSAGTG
          T.DL..LKAVLD.LDALLAQKV.PRRWNLQVL.L.D..G.F..VW.G..ECSSEA....R.T....AG..
Retrocopy TRDLEVLKAVLDRLDALLAQKVPPRRWNLQVLDLQDIKGNFWTVWCGDPECSSEATE-QRPT>QRTAGMR

Parental  RQRPVVVSADLSLTEGNLDPCLTYLVQWVRNRKDALHLCCRKLVISEIAFLNVSEVLEVVDLDCVREVEV
          R.RP..VS..L.LTE..LD..L.YL..WVR..KDA.HLCCRKL.I.E....N...VLE.VDLDC..EV..
Retrocopy RLRPIMVSIELTLTESTLDQWLIYLLWWVRKKKDAFHLCCRKLLIEEMMGQNMRKVLEMVDLDCIQEVKL

Parental  DCSPELSPEPVFAPYLGQMSNLGKLVLCNIFVCPLSSPKEKEQIVARFTSQLFKLHNLRELAVYTGSFLV
          DC...LS....FAPYLGQMS...KL.L.N.......SP...E.I....TSQL.KL.NLR.L..Y...FL.
Retrocopy DCGSDLSTTMGFAPYLGQMSSRSKLDLLNSYELGNNSPNQNE-IISQVTSQLLKLNNLRKLHMYL-CFLR

Parental  FCLHQVLRCLETPLETFLMTKCLLSTSDWENLSSWPSISQLKELRLGGIILAHLSPEPLSLLLEKIAATV
          ..L..VL.C.E.PLET.....C.LS.SDWENLSSWPS.SQLKEL.L..I.L.H.SPEPL.L.LE..A.T.
Retrocopy HSLQ*VLGCFEAPLETLFLNYCNLSASDWENLSSWPSMSQLKELHLEDIALTHFSPEPLKLFLENVAGTG

Parental  QSLFLENCGIMDSQLNVIVPALSRCCQLTTLSFRGNFLSRASLEHLLRHTARLSKLRLEVYPAPLESYDA
          QSL.LE.CG..DSQLNVI.PALS.CCQLTT...RGNF.S.A.LEHLL.HTARLSKL.LEVY.APLESYDA
Retrocopy QSLVLEDCGMVDSQLNVIMPALSCCCQLTT---RGNFFSWATLEHLLHHTARLSKLSLEVYSAPLESYDA

Parental  -RGVLDSRKYEQFRAELTEILRGIRKPKKIVF
          .R.VLDSRKY.QF.AELTEILRGIRKPKKI.F
Retrocopy >RKVLDSRKYYQFQAELTEILRGIRKPKKIAF

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_1100 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,