RetrogeneDB ID: retro_ogar_67

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873767.1:1321860..1323153(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000024066
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSOGAG00000002492
• Aliases: None
• Description: LSM14A, SCD6 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24489]

Sequence

>retro_ogar_67
ATGAGCTGGAAGAACCCTTATATCGGCAGCAAGATCAGCCTCATTTCCAAGGCAGAGATCCGGTATGAAGGCATCCTGTA
CACCATCGACACCGAGAACGCCACTGTAGCCCTTGCCAAAGTTCAATCCTTTGGTACAGAAGACAGACCAACAGACTGTC
CAGTACCACCTGGAGAAGAAGTCTTTGAATACATTATATTCCGCAGGAATGCTATTAAACAGCTTACAGTTTGTGAGCCA
CCAAGACAGTACTCTTTGCCTCTAGACCCAGCCATCGTTCAGTTTTCACTAGGCTCATCTACACTAGGCTCATCTACTTC
GTTCGAGTCATTGGGTTCTTATGGACTTTTTGGTGGAATGCCGGCATACAATCATTTCAATCCGAGTTCATTATTTGGGC
AGCGGTTTGGCGCTGGTAGTGTTGCTGGAAGCTCTTTGACATCCTTTGGGACAGAAACATCAAACAGTGGTAACTTCTCT
CAAAGTAATGCAGTTGGTTCTACCTTTACACAGGATACGAGTTCTCTAAAATCACAGTTATTTCAGGGTCATTCACCCCC
TCAGTTACACCCTTTGAGAAAAAGCCCAATCATGGATCAAGCAGTACAGATTTCCTCAGCCAACTTACCTGCTCCAGCAC
CTATTGGGAGAAGGAGCTCTGTATCAACCAGGCCTTTGCCATCTATCAGCCAAATATCAGTAGAGAATCAAGAGCACAGT
CGAGTATATAAAGCTTCAAGACCAGAAAATGAGCAACTCAGAAAAGATAGCAAAAACCAAGTAGCTCCAGGTGCTCCTTC
ACCTCCAAGAAGAGGGTGTGGGGGTTATCGTGGTGACAGAGGAAAATTTGGTACTTGGGTAGATGTTCCAGTGAAATCTG
AGAAAGATTTTCAAAGTGCAAATGAACAATTTAACAAGGAGGAAATCAACAGAGAGTTTTATAATAAACTTAAATTAAAA
GAAGATAAACCTGAGAAACCAGAGAAGCCTGTAAATCGCAAAGGTAACGGAGACTCAGGAGTTGATACCAAGAAGAATGA
AGGAAATGCCAAAAAGGAAGGTCCACTTGGACCTAATTGCTATTATGACAAAACTAAATCCTTCTTTGATAATATTTCTT
GTGCTGATAATAGAGAACGGAGACCAACTCGGGCTGAAGAAAGAAGACTAAATGCGGAAACATTTGGAACCCCATTTAAT
CCGAACCGTGGCCGTGGGGGGTATAGAAGCAGAGGAGGGGTTGGTTTCCCTAATGATAGAGGGCGTGGTCGTGGGAGAGG
TGGGAACTCTACC

Alignment

ORF - retro_ogar_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.94 %
• Parental protein coverage: 93.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS
          MS...PYIGSKISLISKAEIRYEGILYTIDTEN.TVALAKV.SFGTEDRPTD.P.PP..EVFEYIIFR..
Retrocopy MSWKNPYIGSKISLISKAEIRYEGILYTIDTENATVALAKVQSFGTEDRPTDCPVPPGEEVFEYIIFRRN

Parental  DIKDLTVCEPPKPQCSLPQDPAIVQSSLGS----SASSFQSVGSYGPFGRMPTYSQFSPSSLVGQQFGAV
          .IK.LTVCEPP..Q.SLP.DPAIVQ.SLGS....S..SF.S.GSYG.FG.MP.Y..F.PSSL.GQ.FGA.
Retrocopy AIKQLTVCEPPR-QYSLPLDPAIVQFSLGSSTLGSSTSFESLGSYGLFGGMPAYNHFNPSSLFGQRFGAG

Parental  GVAPQAGSSLTSFGTETSNSGTLSQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTAS
          .V...AGSSLTSFGTETSNSG..SQS.AVGS.FTQDT.SLK.QL.QG.S.PQL.PLRKSP.M.QAVQ..S
Retrocopy SV---AGSSLTSFGTETSNSGNFSQSNAVGSTFTQDTSSLKSQLFQGHSPPQLHPLRKSPIMDQAVQISS

Parental  AHLPAPAPVGRRSPVSTRPLPSTSQKAVENQEHRRAEVHKVSRPENEQLRNDSKRQVAPGAPSVPRRGRG
          A.LPAPAP.GRRS.VSTRPLPS.SQ..VENQEH.R..V.K.SRPENEQLR.DSK.QVAPGAPS.PRRG.G
Retrocopy ANLPAPAPIGRRSSVSTRPLPSISQISVENQEHSR--VYKASRPENEQLRKDSKNQVAPGAPSPPRRGCG

Parental  GHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQDKPVNGEDKGDSGVD
          G.RG.RG.FG...D.P.K.EKDF...SAN.QFNKEEI.REF.NKLKLKEDK.EK..KPVN....GDSGVD
Retrocopy GYRGDRGKFGTWVDVPVKSEKDF--QSANEQFNKEEINREFYNKLKLKEDKPEKPEKPVNRKGNGDSGVD

Parental  TQNSEGNAEEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRG
          T...EGNA..E.PLGPNCYYDKTKSFFDNISC.DNRERRPT.AEERRLNAETFG.P..PNRGRGGYR.RG
Retrocopy TKKNEGNAKKEGPLGPNCYYDKTKSFFDNISCADNRERRPTRAEERRLNAETFGTPFNPNRGRGGYRSRG

Parental  SLGFRGGRGRGGGRGGTFT
          ..GF...RGRG.GRGG..T
Retrocopy GVGFPNDRGRGRGRGGNST

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_67 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67 ,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,