RetrogeneDB ID: retro_mmur_103

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1252:20631..21967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA4A
• Ensembl ID: ENSMICG00000000804
• Aliases: None
• Description: tubulin, alpha 4a [Source:HGNC Symbol;Acc:12407]

Sequence

>retro_mmur_103
ATGCGTGAGTGCATCTCCATCCAGATTGCTGGTGTCCAGGTTGGCAATGCCTGCTAGGAGCTCTACTGCCTGGAACACAG
CATCCAGCCTGATGGCCAGATGCCAAGTGACAGGACCACTGGGGGAGGAGACGACTCCTCCAACACCTTCTTGTGTGAAA
CGGGCTCTGGCAAGCATGTGCCCAGAGCAGTATTTGCAGACCTGAAACCCACAGTCATTGACCAAGTTTGCACTGGTACC
TACTGCCAGCTTGTATACTGAGCAGCTCATCACAGGAAAGAAAGATGCTGCCAATAACTATGCCCGTGGGCACTACACCA
TCGGCAAGGAGATCACTTACCTCCTCTTGAACCAAACACACAAGCTGGCCGACCAGTGCACAGGTCTTTAGGGATTCTGG
GTTTTCCACAGCTTTGGTGGGGGAATTGGTTCTGGGTTCACTTCCCTGCTGATGCAACACCTCTCTGTTGATTAAGGCAA
GAAGTCCAAGCTGAAGCTCTCCATGTACCCAGGCCCCCAGGTGTCCACAGTTGTAGTTGAGCCCTACAGGTCCATCCTCA
CCACCCATACCACCCTGAAGCACTCTGATTGTGCTTTCATGATAGACAATGAGGCCACCTAAGACATCTGTTGTAGAAAC
TTCAATATTGAGCACCCAACCTACACCAACCTTAACTGCTTTATTGGCTAGAATGTGTCCTTCATCACTTCTTCCCTCAG
AATTGATAGAACCCTGAATATTGATCTGTCAGAATTCCAGACCAACCTGGTGCCCTATCTCCACCTCCACTTCCCTCTGG
CCACATATATGCCCCTGTGATCTCTGCTGGGAAAGCCTACATGAACAGCTTACTGTGGCAGAGATCACCAATGCCTTTTT
TGAGCCAACCAACCACATAGCAAAATGTGACCCTCGCTGTGGTAAATACATGGCTAGCTGGCTGTTGTAAAAGCGGTGAT
GTGGCCCCCAAAGATGTCATTGTTGCCAATAATACCATCAAGACCAAGCATACCATCTGGTGTGTGGATTGGTGTTCCAT
TGGCTTCAAGGTTGGCATCAATCACAGCCTCCCCCATGGTACCTGGTAGAGAGCTGGCCAAGGTGCAGAGAGCTGTGTGC
ATGTTGAGCGACACCACAGCAGTTGCCCAGGCCTGGGCTCACCTGGACCACTAGTTCAACCTGATGTATGCCAGGCATGC
CTTTGGTCACTGGTACATGGGTTGGGGGATAGAGGAAGGAGAGTTTTCTGAAGTCCATGAGGACATGGCTGCCTTTGACA
GGGATTAGGAGGAGGTTGGAGCAGATAATCCTGAGGGAAAGGATGAGGGTGAAGAA

Alignment

ORF - retro_mmur_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 9
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDL
          MRECIS.....AGVQ.GNAC.ELYCLEH.IQPDGQMPSD.T.GGGDDS..TF.CETG.GKHVPRAVF.DL
Retrocopy MRECISIQI--AGVQVGNAC*ELYCLEHSIQPDGQMPSDRTTGGGDDSSNTFLCETGSGKHVPRAVFADL

Parental  EPTVIDEIRNG-PYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVL-RIRKLSDQCTGLQGFLVFH
          .PTVID....G.P...L...EQLITGK.DAANNYARGHYTIGKEI....L....KL.DQCTGL.GF.VFH
Retrocopy KPTVIDQVCTG>PTASLY-TEQLITGKKDAANNYARGHYTIGKEITYLLLNQTHKLADQCTGL*GFWVFH

Parental  SFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAI
          SFGGG.GSGFTSLLM..LSVD.GKKSKL..S.YP.PQVST.VVEPY.SILTTHTTL.HSDCAFM.DNEA.
Retrocopy SFGGGIGSGFTSLLMQHLSVD*GKKSKLKLSMYPGPQVSTVVVEPYRSILTTHTTLKHSDCAFMIDNEAT

Parental  YDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIS-A
          .DIC.RN..IE.PTYTNLN..I...VS.IT.SLR.D..LN.DL.EFQTNLVPY...HFPLATY.P..S..
Retrocopy *DICCRNFNIEHPTYTNLNCFIG*NVSFITSSLRIDRTLNIDLSEFQTNLVPYLHLHFPLATYMPL*S>C

Parental  EKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR-GDVVPKDVNAAIAAIKTKRSIQFVDWC
          ....HEQL.VAEITNA.FEP.N...KCDPR.GKYMA..LL...GDV.PKDV..A...IKTK..I..VDWC
Retrocopy WESLHEQLTVAEITNAFFEPTNHIAKCDPRCGKYMASWLL*K>GDVAPKDVIVANNTIKTKHTIWCVDWC

Parental  PTGFKVGINY-QPP-TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEE
          ..GFKVGIN..QPP...VPG..LAKVQRAVCMLS.TTA.A.AWA.LDH.F.LMYA..AF.HWY.G.G.EE
Retrocopy SIGFKVGINH<QPP<PMVPGRELAKVQRAVCMLSDTTAVAQAWAHLDH*FNLMYARHAFGHWYMGWGIEE

Parental  GEFSEAREDMAALEKDYEEVGIDSYEDEDEGEE
          GEFSE..EDMAA...D.EEVG.D..E..DEGEE
Retrocopy GEFSEVHEDMAAFDRD*EEVGADNPEGKDEGEE

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_103 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_103 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.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103 ,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,