RetrogeneDB ID: retro_mmur_1605

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_9176:10628..11864(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSMICG00000011598
• Aliases: None
• Description: LSM14A, SCD6 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24489]

Sequence

>retro_mmur_1605
CGATCCTTTGGTACAGAAGACAGACCAACAGATTACCCAGTCCCACCTCAAGATGAAGTCTTTGAGTACATTATATTCCG
CAGGAGTGCTATTAAAGAGCTCACTGTTCATGAGCCACCAAAACCACAGTGTTACTTGCCTCAAGACCCAGCGATCATTC
AGTCTTCACTAGGCTCATCTACTTCTCCATTGCAGTCAGAGGGTTCTTATGGACCTTTCGGCAGGATGTCGACGTACAGT
CAGTTCAGTCCAAGTTCATTAGGCGGGCAGCAGTTTGGCGCTGTTGGTGGTGCTGGAAGCTCCTTGACATCCTTTGGAAC
AGAAACATCAAACAGTGGTACATTATACCAAACGAGTGCAGCTGATTTTGACTTTACACAAGATACAACATCTCTAAAAA
TGCAGTTATATCAAAGTCCTTCAAGCCCTCTGTTAGACCTTTTGAGAAAAAGCCCAACCATGGAACAAGCAGTACAGACT
CCCTCAGCCAACTTACCTGCTCCAGCATCTGTTGAGAGAAGGAGCCTTGTATCAACAAGGCCTTTGCCATCTAGCAGCCA
AAAACCAGCAGAGAATCAAGAGCACAGGCAAGCTGAAATACACAAAGTTTCAAGGCCTGAAAATGAGCAACTCAGAAATG
ATAGCAAAGGACAAATAACTCCAGATGCTACTTTGGCTCCAAGAAGAGAGTGTGGAGGTCAACCAGATAGCAGGGGAAGA
TTTGGTGTATGGCAAAATGGCCTAGTGATGTTTGAGAAAGACTTTGAAACTGCAAATGCACAATTTAACAAGGAAGAGAT
CGACAGAGAGTTTCATAATAAACTTAAATTAAAAGAAGATAAACTTGAGAAACAGAAGGAGCCTGTGAATGGTGAAGGTA
AAGGAGACTCAGGAGTGGATACCCAGAAGAGTAAAGGAAATGTCAATGAAAAAAGTCCACTTGGACCTAATTGCTATTAT
GACAAAACTAAATCCTTCTTTGATAATATTTCTTGTGATGGTAATACGGAGCGGAGACTAACCTGGGCTCAAGAAAGAAG
ATTAAATGCTGAAACATTTGGAACCCACCATCGTCCAAACCGTGGCCGTGGGAAGTACAGAGGCAGAGGTATTGGTTTCT
TTAATGGCAGAGGACGTGGTGGTGGCAGAGGTGGTGCCTTCACCACCCGTTGAGGATTTCATCGTGGATTCAGAGGAAGG
CATGGGGGCAGGGAGTTTGAAGATTTTGAATATAAG

Alignment

ORF - retro_mmur_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSASSFQSVGSY
          RSFGTEDRPTD.P.PP.DEVFEYIIFR.S.IK.LTV.EPPKPQC.LPQDPAI.QSSLGSS.S..QS.GSY
Retrocopy RSFGTEDRPTDYPVPPQDEVFEYIIFRRSAIKELTVHEPPKPQCYLPQDPAIIQSSLGSSTSPLQSEGSY

Parental  GPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLPHSSAAGSAFTQDTRSLKTQPSQGR
          GPFGRM.TYSQFSPSSL.GQQFGAVG.AGSSLTSFGTETSNSGTL...SAA...FTQDT.SLK.Q..Q..
Retrocopy GPFGRMSTYSQFSPSSLGGQQFGAVGGAGSSLTSFGTETSNSGTLYQTSAADFDFTQDTTSLKMQLYQSP

Parental  SSPQLDPLRKSPTMEQAVQTASAHLPAPAPVGRRSPVSTRPLPSTSQKXXXXXXXXXXEVHKVSRPENEQ
          SSP.LD.LRKSPTMEQAVQT.SA.LPAPA.V.RRS.VSTRPLPS.SQK..........E.HKVSRPENEQ
Retrocopy SSPLLDLLRKSPTMEQAVQTPSANLPAPASVERRSLVSTRPLPSSSQKPAENQEHRQAEIHKVSRPENEQ

Parental  LRNDSKRQVAPGPPSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLK
          LRNDSK.Q..P....APRR..GG....RGRFG....G...FEK..DFE.ANAQFNKEEIDREFHNKLKLK
Retrocopy LRNDSKGQITPDATLAPRRECGGQPDSRGRFGVWQNGLVMFEK--DFETANAQFNKEEIDREFHNKLKLK

Parental  EDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRL
          EDKLEKQ..PVNGE.KGDSGVDTQ.S.GN..E..PLGPNCYYDKTKSFFDNISCD.N.ERR.TWA.ERRL
Retrocopy EDKLEKQKEPVNGEGKGDSGVDTQKSKGNVNEKSPLGPNCYYDKTKSFFDNISCDGNTERRLTWAQERRL

Parental  NAETFGIPLRPNRGRGGYRGRGGLGFRGGRGRGGGRGGTFTTPRGFRGGFRGGRGGREFADFEYR
          NAETFG...RPNRGRG.YRGR.G.GF..GRGRGGGRGG.FTT..GF..GFRG..GGREF.DFEY.
Retrocopy NAETFGTHHRPNRGRGKYRGR-GIGFFNGRGRGGGRGGAFTTR*GFHRGFRGRHGGREFEDFEYK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1605 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1605 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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,