RetrogeneDB ID: retro_mluc_1011

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429788:3184538..3185806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSDE1
• Ensembl ID: ENSMLUG00000005681
• Aliases: None
• Description: None

Sequence

>retro_mluc_1011
ATGTTCTTCCACTATAGCGAAATTCTGGACGGGAACCAGCTCCATACTGCAGATGAAGTAAAGTTTACTGTGGTTCCTGA
TATGCTCTCTGCCCAAAGAAATCATGCTATTAGAATTTAAAAAAACTTCCCAAGGGCATGGTTTCATTCCATTTCCATTC
AAATCATCATTTTCTGGGCATTATAGAAAAAGAAGCCACTTTTTCCATTTCTAAAACCACTAGCCAAAATAAAGGCAAGG
AAACGGAGACTGAGGATGGTATTATTGCTTATGATGACTGTGGGGTGAAATTGACTATTTTTTTTCAAGCCAAGGATGTG
AACGGATCTACTTCTCCTCAAATAGGTGATAAGGTTGAATTTAGTATTAGTGACAAACAGAGGCCTGGACAGCAGACTGT
AACCTGTGTGCAACTTTTAGATCATAATTCTAACTCCAAGAGGCTCTTAGGTTATGTGGCAATTCTGAAGGATACTTTTG
GATTTATTGAAACAGCCAATCATGATTAGGACATATTTTTCCATTACAGTGAGTTCTCTGGTGATGCTGATAGCCTAGAA
CTGGGGGACATGGTCAAGTACAACTGGTCCAAAGGCAAAAGCAATAAAGTCAGTGCAGAAAAAGTCAACAAAACACACTT
GGTGAATGGCCTTACTGAAGAAGCAGATCCTACATCTACTCTGGTAAAGTCATTCGCCCCTTGAGAAGTGTTGATCCAAC
ACAGACTGAGTACCAAGGAATGATTGAGACTGTGGAGAAAGGGGATATGAAAGGTAAGGTCTATCCATCTGGCATAGTTG
GAATGGCCAACAAAGGAGATTGCCTGCAGATAGAGAAGAGTGTAAAATTCCATTTGTGTGTCCTAGGCCAAAATGCACAG
TCTATGGCTTACAACATCACCCTTCTGTGTAGGGCCACTGTGGAGTGTGTGAAAAATCAGTTTGGCTTCATTATTATGAA
GTAGGAGATAGCAAGAAGCTCTTTTTCCATGTGAAAGATGTTCAGGATGGCATTGAGCTACAGGCTAGAGATGAGGTGAT
TCTTAATCAGCACACTGGCAAGTGCAGTGTTTGTAATGTTTGGCGAGTCTGCAAGGGCCCCAAGGCTGTTGTAGCTTCAC
TACCTGATAGGTTGGTCAATCGCTTGAGGAACATCACCCTGGATAATGCCAGTGCTCCTGGCTAATGGTTCTTCCTCAGC
CAAAGGGACCAGATAACTCAATGGGACTTGGTGTAGAACGAAAGAACTGTCCGGCTGTTGTCATTGAC

Alignment

ORF - retro_mluc_1011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.41 %
• Parental protein coverage: 52.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MFFHYSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRI-KKLP-KGTVSFHSHSDHRFLGTVEKEATFS
          MFFHYSEILDGNQLH.ADEV.FTVVPDMLSAQRNHAIRI.K..P.KG.VSFH.HS.H.FLG..EKEATFS
Retrocopy MFFHYSEILDGNQLHTADEVKFTVVPDMLSAQRNHAIRI*KNFP<KGMVSFHFHSNHHFLGIIEKEATFS

Parental  NPKTTSPNKGKEKEAEDGIIAYDDCGVKLTIAFQAKDVDGSTSPQIGDKVEFSISDKQRPGQQIATCVRL
          ..KTTS.NKGKE.E.EDGIIAYDDCGVKLT...QAKDV.GSTSPQIGDKVEFSISDKQRPGQQ..TCV.L
Retrocopy ISKTTSQNKGKETETEDGIIAYDDCGVKLTXXXQAKDVNGSTSPQIGDKVEFSISDKQRPGQQTVTCVQL

Parental  LGRNSNSKRLLGYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAEKV
          L..NSNSKRLLGYVA.LKD.FGFIETANHD..IFFHYSEFSGD.DSLELGDMV.Y..SKGK.NKVSAEKV
Retrocopy LDHNSNSKRLLGYVAILKDTFGFIETANHD*DIFFHYSEFSGDADSLELGDMVKYNWSKGKSNKVSAEKV

Parental  NKTHSVNGITEEADPT-IYSGKVIRPLRSVDPTQTEYQGMIEIMEEGDMKGEVYPFGIVGMANKGDCLQK
          NKTH.VNG.TEEADPT.IYSGKVIRPLRSVDPTQTEYQGMIE..E.GDMKG.VYP.GIVGMANKGDCLQ.
Retrocopy NKTHLVNGLTEEADPT<IYSGKVIRPLRSVDPTQTEYQGMIETVEKGDMKGKVYPSGIVGMANKGDCLQI

Parental  GESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFI-NYEVGDSKKLFFHVKEVQDGIELQAGDEV
          ..SVKF.LCVLGQNAQ.MAYNIT.L.RATVECVK.QFGFI..YEVGDSKKLFFHVK.VQDGIELQA.DEV
Retrocopy EKSVKFHLCVLGQNAQSMAYNITLLCRATVECVKNQFGFI<YYEVGDSKKLFFHVKDVQDGIELQARDEV

Parental  EFSVILNQRTGKCSACNVWRVCEGPKAVAAPRPDRLVNRLKNITLDDASAPR-LMVLRQPRGPDNSMGFG
          ....ILNQ.TGKCS.CNVWRVC.GPKAV.A..PDRLVNRL.NITLD.ASAP..LMVL.QP.GPDNSMG.G
Retrocopy ----ILNQHTGKCSVCNVWRVCKGPKAVVASLPDRLVNRLRNITLDNASAPG<LMVLPQPKGPDNSMGLG

Parental  VERKIRQAGVID
          VERK...A.VID
Retrocopy VERKNCPAVVID

Legend:

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

Expression

RNA-Seq

Myotis lucifugus was not studied using RNA-Seq expression data.

ChIP-Seq

Myotis lucifugus was not studied using ChIP-Seq data.

EST

Myotis lucifugus was not studied using EST data.

TSS

Myotis lucifugus was not studied using FANTOM5 data.

Lab

retro_mluc_1011 was not experimentally validated.

Homology

Retrocopy orthology:

Myotis lucifugus 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017129	1 retrocopy	retro_amel_1392,
Cavia porcellus	ENSCPOG00000000538	2 retrocopies	retro_cpor_1402, retro_cpor_513,
Myotis lucifugus	ENSMLUG00000005681	1 retrocopy	retro_mluc_1011 ,
Mus musculus	ENSMUSG00000068823	1 retrocopy	retro_mmus_1757,
Rattus norvegicus	ENSRNOG00000030302	1 retrocopy	retro_rnor_1429,