RetrogeneDB ID: retro_mmur_42

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_7370:53588..55181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMICG00000000431
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PABPC1L
• Ensembl ID: ENSMICG00000000974
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]

Sequence

>retro_mmur_42
ATGAACGCTGCGGCCAGCAGCTACCCCATGGCCTCCCTGTACGTGGGTGACCTGCACTCGGACGTCACCGAGGCCATGCT
GTATGAAAAGTTCAGCCCTGCGGGGCCTGTGCTGTCCATCCGGGTCTGTCGAGATATGATCACTCGCCGCTCCCTGGGTT
ATGCCTACGTCAACTTCCAGCAGCCAGCTGACGCTGAGCGGGCCTTGGACACCATGAACTTTGATGTGATTAAAGGAAAG
CCAATCCGTATCATGTGGTCTCAGAGGGATCCCTCTTTGAGAAAGTCTGGTGTGGGAAACGTCTTCATCAAGAACCTGGA
CAAATCTATAGATAACAAGGCACTTTATGATACTTTTTCTGCTTTTGGAAACATTCTGTCCTGTAAGGTGGTGTGTGATG
AGAACGGCTCTAAGGGTTATGCTTTTGTCCACTTCGAAACCCAAGAGGCTGCCGACAAGGCCATCGAGAAGATGAATGGC
ATGCTCCTCAATGACCGCAAAGTGTTTGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCTGAGCTTGGAGCCAAAGC
CAAGGAATTTACCAATGTGTATATCAAGAACTTTGGGGAAGAGGTGGATGATGAGAGTCTGAAAGAGCTATTCAGCCAGT
TTGGTAAGACACTAAGTGTCAAGGTGATGAGAGATCCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTCAGTTACGAAAAA
CACGAGGATGCCAATAAGGCTGTGGAAGAGATGAATGGAAAAGAAATCAGTGGTAAAGTCATATTTGTAGGCCGTGCTCA
GAAGAAAGTGGAACGGCAGGCAGAGTTAAAACGGAAATTTGAGCAGCTGAAACAGGAGAGAATTAGTCGATATCAGGGGG
TGAATCTCTACATTAAGAACTTGGATGACACTATTGATGATGAGAAATTAAGGAAAGAGTTTTCTCCTTTTGGATCAATC
ACCAGTGCTAAGGTGATGCTGGAAGATGGAAGAAGCAAAGGGTTTGGCTTCGTCTGCTTCTCATCTCCTGAAGAGGCAAC
CAAAGCAGTCACTGAGATGAATGGACGCATCGTGGGCTCCAAGCCACTGTATGTTGCCCTGGCCCAGAGGAAGGAAGAGA
GAAAGGCTCACCTGACCAACCAATATATGCAGCGGGTGGCTGGAATGAGAGCACTCCCTGCCAATGCCATCTTAAATCAG
TTCCAGCCTGCAGCTGGTGGCTACTTTGTGCCAGCAGTCCCACAGGCTCAAGGAAGACCTCCGTATTATACACCTAACCA
GTTAGCACAGATGAGGCCTAATCCACGCTGGCAGCAAGGCGGGAGACCTCAAGGCTTCCAAGGAATGCCAAGTGCTATAC
GCCAGTCTGGGCCTCGTCCAACTCTTCGCCATCTGGCTCCAACTGGTAATGCTCCGGCCTCTCGTGGCCTCCCTACTACT
ACTCAGAGAGTCGGGTCTGAGTGCCCGGACCGCTTGGCTATGGACTTTGGTGGGGCTGGTGCCGCCCAGCAAGGGCTGAC
TGACAGCTGCCAGTCTGGAGGCGTTCCCACAGCCGTGCAGAACTTAGCGCCTCGTGCTGCTGTCACTGCTGCT

Alignment

ORF - retro_mmur_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 71.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNASSSGYPLASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDVATRRSLGYAYINFQQPADAERALD
          MNA..S.YP.ASLYVGDLH.DVTEAMLYEKFSPAGP.LSIRVCRD..TRRSLGYAY.NFQQPADAERALD
Retrocopy MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD

Parental  TMNFEMLKGQPIRMMWSQRDPGLRKSGVGNIFIKNLEDSIDSKALYDTFSTFGNILSCKVACDEHGSRGF
          TMNF...KG.PIR.MWSQRDP.LRKSGVGN.FIKNL..SID.KALYDTFS.FGNILSCKV.CDE.GS.G.
Retrocopy TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY

Parental  GFVHFETQEAAQNAISTMNGMLLNDRKVFVGDFKSRREREVELG-RAMEFTNIYVKNLKADVDEHGLQEL
          .FVHFETQEAA..AI..MNGMLLNDRKVFVG.FKSR.ERE.ELG..A.EFTN.Y.KN....VD...L.EL
Retrocopy AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL

Parental  FSQFGKTLSVKVMRDNGGHSRGFGFVNFEKHEEAQKAVVHMNGKEVSGQLLYVGRAQKRVERQKELKRRF
          FSQFGKTLSVKVMRD..G.S.GFGFV..EKHE.A.KAV..MNGKE.SG....VGRAQK.VERQ.ELKR.F
Retrocopy FSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKF

Parental  EQMKQDRLKRYQGVNLYVKNLDDSIDDEKLRKEFSPYGVITSAKVMTEGGHSRWFGFVCFSSPEEATKAV
          EQ.KQ.R..RYQGVNLY.KNLDD.IDDEKLRKEFSP.G.ITSAKVM.E.G.S..FGFVCFSSPEEATKAV
Retrocopy EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVGTKPLYVALAQRKEERKAILTNQYMQRLSTMRALGSPFLGSSFQQPT-TYFLPAVPQPPAQA
          TEMNGRIVG.KPLYVALAQRKEERKA.LTNQYMQR...MRAL........FQ.....YF.PAVPQ.....
Retrocopy TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPAAGGYFVPAVPQAQGRP

Parental  AYYGSSPAPPPQPAPRW
          .YY.........P.PRW
Retrocopy PYYTPNQLAQMRPNPRW

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_42 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_42 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007905	6 retrocopies	retro_meug_1165, retro_meug_1229, retro_meug_1274, retro_meug_1343, retro_meug_419, retro_meug_987,
Microcebus murinus	ENSMICG00000000974	1 retrocopy	retro_mmur_42 ,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000006324	1 retrocopy	retro_mluc_509,