RetrogeneDB ID: retro_mluc_1727

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429895:3251649..3253649(+)
• Located in intron of: ENSMLUG00000003515

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP1
• Ensembl ID: ENSMLUG00000012439
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G1PKJ9]

Sequence

>retro_mluc_1727
ATGGCTGGTATCATACCTAATGAAAGTAATGGGCTTTCAAGAGGTAGTCCATCAAAGAAAAACAGACTTTCCTCTACGTT
TTTTCAGAAAAAGGGAACTAAGAGAGCCTTGGATTTCACAGATTCTCAAGAAAATGAAGAAAAGGTTTCTTCTGATTATA
GAGGATCTGAAATTGATCAAGTTGTTCCTGCGGCACAGTCCTCACCTATGAATTGTGAGAAGAGAGAAAACTTGTTACCA
TTTGTGGGGCTAAATAATCTCGGCAATACTTGTTATCTTAATAGTATACTTCAGGTATTATATTTTTGTCCTGGTTTTAA
ATCTGGAGTGAAGCACTTATTTAATATTATTTCAAGGAAGAAAGAAGCTCTGAAAGATGAAGCCAATCAAAAAGAGAAGG
GAAATTGTCAAGAAGATTCTTTGGCAAGTTATGAACTAATATGCAGTTTACAGTCCTTAATCATTTCAGCTGAACAGCTT
CAGGCTAGTTTTCTTTTAAATCCAGAAAAATACACTGATGAACTTGCTACTCAGCCAAGACGATTATTTAACACACTCAA
GGAACTCAACCCTATGTATGAAGGATATCTACAGCATGATGCACAGGAAGTATTACAGTGTATTTTGGGAAACATTCAAG
AAACATGCCAACTCCTAAAAAAAGAAGAAGTAAAAAATGTGGCAGAATTATCTGACAAGGTAGAAGAAAAACCTAATCAG
AGAGAGGCAATTAATGGGGTCAATAGCACAGAGATGGACAATATGGGGCATACTGAAGACTATAAAGAAAAACTCCCAAA
AGGAAATGGGAAGAGAAAAAGTGACACTGAATTTGGTAACATGAAAAAAAAAGTTAAGGTATCCAAGGAACACCAGTCAT
TGGAAGAGAACCGGAGACAAACCAGATCAAAAAGAAAAGCTACAGGTGATATATTAGAGATTCCTCCTAAAATAGTCACT
AAGCACATTCCTGAAAATGAGAGTGCAAGACCCTCACAGAAGAAATCAAAAGTTAAAACAAGTTGGTTAAAGTCTGCAAC
TAAGCAACCCAGCATCTTTTCTAAATTCTGTAGTCTGGGGAAATAAACCAAGGATCAAAGGACACCCTAAAGAAAATGAA
TATGATCTGAAGAGGACTCTGGGAAGTGTGAAAATGATCACACAATTAATGGCTGTGGACTTGAATCTCCAGGAAATAAT
GTTAAGTCCACTAATGGTGATGAAGTTAAGCCCATCAACAAAGGCACAGAGCAAATGGGTTTTGAGCTTGTAGAGAAGTT
ATTTCAAGGTCAGCTGGTATTCAGAACTCGTTGTTTAGAATGTGAAAGTTTAACAGAAAGAAGAGAAGATTTTCGAGACA
TCAGTGTGCCAGTACAAGAAGATGAGCTTTCTAAAGTAGAGGAGAGTTCTGAAAGTTCTCTAGAGCCAAAAACAGAAACG
AAGACCCTGAGGTGGGCAATTTCACAATTTGCTTCAGTGGAGAGGCTTGCAGGAGAAAATAAATATTTCTGTGAAAATTG
CCATCACTATACTGAAGCTGAACGAAGTGTTTTGTTTGACAAAATGCCTGAAGTTTTAACCATTCATTTGAAGTGTTTTG
CTGCTAGTGGCTTGGAGTTTGCTTGTTATGGTGGTGGACTTTCCAAGATCAACACTCCTTTACTGACACCTCTCAAACTG
TCACTAGAAGAATGGAGTACAAAGCCGACCAATGACAGCTATGGATTATTTGCAGTTGTGATGCATAGTGGCACTACAAT
TAGTAGTGGGCACTACACTGCTTCTGGTTAAAGTCACAGACCTTAACAGTTTAGAACTAGATGAGGGAAAGTTTTGTGCT
TTGACCAGTTGTGTGAAATGAGTAAGCCAGAACCCACGGAATGAGGGAGGAAGCCAGGGGGATTGGCTGAAAAATTACGA
TGGATGAAGTTGTCCAATGAGAGTCCCTTGGGAAACAACACAGCCCGAGAAAGGTTTTGAACAAAAAAAAATGAGAAAGC

Alignment

ORF - retro_mluc_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.25 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  MPGVIPNESNGLSRGSPSKKNRLSLKFFQKKETKRALDFTDSQENEEKVSSDYRGSEIDQVVPAAQSSPM
          M.G.IPNESNGLSRGSPSKKNRLS..FFQKK.TKRALDFTDSQENEEKVSSDYRGSEIDQVVPAAQSSPM
Retrocopy MAGIIPNESNGLSRGSPSKKNRLSSTFFQKKGTKRALDFTDSQENEEKVSSDYRGSEIDQVVPAAQSSPM

Parental  NCEKRENLLPFVGLNNLGNTCYLNSILQVLYFCPGFKSGVKHLFNVISRKKEALKDEANQKEKGNCKEDS
          NCEKRENLLPFVGLNNLGNTCYLNSILQVLYFCPGFKSGVKHLFN.ISRKKEALKDEANQKEKGNC.EDS
Retrocopy NCEKRENLLPFVGLNNLGNTCYLNSILQVLYFCPGFKSGVKHLFNIISRKKEALKDEANQKEKGNCQEDS

Parental  LASYELICSLQSLIISVEQLQASFLLNPEKYTDELATQPRRLLNTLSRELNPMYEGYLQHDAQEVLQCIL
          LASYELICSLQSLIIS.EQLQASFLLNPEKYTDELATQPRRL.NTL..ELNPMYEGYLQHDAQEVLQCIL
Retrocopy LASYELICSLQSLIISAEQLQASFLLNPEKYTDELATQPRRLFNTL-KELNPMYEGYLQHDAQEVLQCIL

Parental  GNIQETCQLLKKEEVKNVAELSNKVEEKPNQREAINGVNSTEMDNMGHAEDYKEKLPKGNGKRKSDTEFG
          GNIQETCQLLKKEEVKNVAELS.KVEEKPNQREAINGVNSTEMDNMGH.EDYKEKLPKGNGKRKSDTEFG
Retrocopy GNIQETCQLLKKEEVKNVAELSDKVEEKPNQREAINGVNSTEMDNMGHTEDYKEKLPKGNGKRKSDTEFG

Parental  NMKKKVKVSKEHQSLEENQRQTRSKRKATGDILEIPPKIVTKHIPENESARPSQKKSKVKISWLKSATKQ
          NM...VKVSKEHQSLEEN.RQTRSKRKATGDILEIPPKIVTKHIPENESARPSQKKSKVK.SWLKSATKQ
Retrocopy NMXXXVKVSKEHQSLEENRRQTRSKRKATGDILEIPPKIVTKHIPENESARPSQKKSKVKTSWLKSATKQ

Parental  PSILSKFCSLGK-INQGSK-GQSKENEYDL-EEDSGKCENDNTINGCGLESPGNNVKSINGNEVKPINKG
          PSI.SKFCSLGK.INQGSK.G..KENEYDL.EEDSGKCEND.TINGCGLESPGNNVKS.NG.EVKPINKG
Retrocopy PSIFSKFCSLGK<INQGSK<GHPKENEYDL<EEDSGKCENDHTINGCGLESPGNNVKSTNGDEVKPINKG

Parental  TEQIGFELVEKLFQGQLVLRTRCLECESLTERREDFQDISVPVQEDELSKVEESSEISPEPKTEMKTLRW
          TEQ.GFELVEKLFQGQLV.RTRCLECESLTERREDF.DISVPVQEDELSKVEESSE.S.EPKTE.KTLRW
Retrocopy TEQMGFELVEKLFQGQLVFRTRCLECESLTERREDFRDISVPVQEDELSKVEESSESSLEPKTETKTLRW

Parental  AISQFASVERIVGEDKYFCENCHHYTEAERSLLFDKMPEVITIHLKCFAASGLEFDCYGGGLSKINTPLL
          AISQFASVER..GE.KYFCENCHHYTEAERS.LFDKMPEV.TIHLKCFAASGLEF.CYGGGLSKINTPLL
Retrocopy AISQFASVERLAGENKYFCENCHHYTEAERSVLFDKMPEVLTIHLKCFAASGLEFACYGGGLSKINTPLL

Parental  TPLKLSLEEWSTKPTNDSYGLFAVVMHSGITISSGHYTAS-VKVTDLNSLELDKG-NFVL-DQLCEMSKP
          TPLKLSLEEWSTKPTNDSYGLFAVVMHSG.TISSGHYTAS.VKVTDLNSLELD.G..FVL.DQLCEMSKP
Retrocopy TPLKLSLEEWSTKPTNDSYGLFAVVMHSGTTISSGHYTAS>VKVTDLNSLELDEG>SFVL>DQLCEMSKP

Parental  EPL-NE-EEAR-GMAE-NYDD-EVSIRVNGNT-QPTK-VLNKKNVEA
          EP..NE.EEAR.G.AE.NYD......RV...T.QP.K.VLNKK..E.
Retrocopy EPT>NE>EEAR>GLAE>NYDG*SCPMRVPWETTQPEK>VLNKKK*ES

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_1727 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012439	1 retrocopy	retro_mluc_1727 ,
Mus musculus	ENSMUSG00000028560	1 retrocopy	retro_mmus_2136,
Otolemur garnettii	ENSOGAG00000009357	1 retrocopy	retro_ogar_3339,
Tursiops truncatus	ENSTTRG00000013871	1 retrocopy	retro_ttru_554,