RetrogeneDB ID: retro_mmur_262

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2054:272376..273814(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PACSIN2
• Ensembl ID: ENSMICG00000012990
• Aliases: None
• Description: protein kinase C and casein kinase substrate in neurons 2 [Source:HGNC Symbol;Acc:8571]

Sequence

>retro_mmur_262
ATGTCTGTCATGTATGATGATTCCGTTGGAGTAGAATTGTCCAGCGATAGCTTCTGGGAGTTTGGGAACTATAAGCGGAC
CGTGAAGCGGATTGACGATGGCCACTGCCTGTGCGGTGACCTCATGAACTGCCTGCACGAATGGGCACGCATTGAGAAGG
CGTACGCACAGCAGCTCACCAAGTAGGCCCGGCGCTGGAGGCAGCTTGTGGAGAAGGAGCCACAATATGGGACGGTGGAG
AAGGCCTAGATGGCCATGATGTACGAGGCAGAGAGGGTGAGCAAGCTACACCTCGAGGTGAAGGCCTCGCTGATGAATGA
AGACTTTGAGAAAATCAAGCACTGGCAGAAGGAAGCCTTCACAAGCAGATGATGGGGGCCTTAAGGAAGACAGAAGCTGA
GACGGCTTCGCAGCACAGAGCCTGGGCAAGAAGCTGAAAGAGTGAGCAGCAAAGAAAGCCCATCACACCAGCGTGCAAAG
AGAGAAGTGAGCATCTCATGAGGAGGCCAACAGCAAAGCAGACCTGTCCCTCAACCCTGAACAGCTTAAGAAATTGCAAG
ACAAAGTAGAAAAATGCAAGCAAGATGTCCTTAAGACCAAAGAGAAGTATGAGAAGTCCCTGAAGGAGCTTGACCAGGGC
ACACCCCAGTACATGGCGAACATGGAGCAGGTGTTTGAACAGTGCCAGCAATTTGAGGAGAAGCGCCTGTGCTTCTGGGA
GGTTCTGCTGGAGGTTCAGAAGCACCTAGACCTGTCCAATGTGGCCAGCTACAAAACCATTTACCGCGACCTGGAGCAGA
GCATCAGGGCAGCCGACGCGATGGAGGACCTGAGGTGGTTCAGAGCCAATCATGGGCCCCGCATGGCCATGAACTGGTCG
CAGTTTGAGGAGTGGTCTGCAGACCTGAATCGAACTCTCAGCCGGAGAGAGAAGAAGACTGCTGACGGTGTCACCCTGAC
AGGCATCAACCAGACAGGCGACCAGTCTCTGCAGAACAAGCCCAGCAGCAACCTTAGTGTCCTGAGCAACCCTGTGCAAT
CCATGCAGTCACAGTCCAGCTACAACCCCTTCGAGGACGAGGACGACACAGGCAGCACCGTCAGTGAGAAGGAGGACATT
AAGACCAAAAATGTGAGCAGCTTCGAGAAGACCCAGAGCTACCCCACCGACTGGTCAGATGATGAGTCCAACAACCCCTT
CTTCTCCACGGATGCCAACGGAGATTCAAACCCGCTTGACGAGGACACCACTTCAGGGATGGAAGTGCGAGTCCAGGCCC
TTTATGACTACGAGGGCCAGGAGCATGACGAGCTGAGCTTCAAGGCTGGGGATGACCTGACCAAGATGGAGGATGAAGAT
GAGCAAGGCTGGTGCAAGGGACGCTCGGACAGTGGGCAGGTTGGCCTGTACCCTGCGAATTACGTGGAGGCGATCCAG

Alignment

ORF - retro_mmur_262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVTYDDSVGVEVSSDSFWEVGNYKRTVKRIDDGHRLCSDLMNCLHERARIEKAYAQQLTEWARRWRQLV
          MSV.YDDSVGVE.SSDSFWE.GNYKRTVKRIDDGH.LC.DLMNCLHE.ARIEKAYAQQLT..ARRWRQLV
Retrocopy MSVMYDDSVGVELSSDSFWEFGNYKRTVKRIDDGHCLCGDLMNCLHEWARIEKAYAQQLTK*ARRWRQLV

Parental  EKGPQYGTVEKAWIAMMSEAERVSELHLEVKASLMNEDFEKIKNWQKEAF-HKQMMGGFKETKEAE-DGF
          EK.PQYGTVEKA..AMM.EAERVS.LHLEVKASLMNEDFEKIK.WQKEAF.HKQMMG....T.EAE.DGF
Retrocopy EKEPQYGTVEKA*MAMMYEAERVSKLHLEVKASLMNEDFEKIKHWQKEAF<HKQMMGALRKT-EAE<DGF

Parental  RKAQKPWAKKLKEVEAAKKAHHTACKEEKLAISREANSKADPSLNPEQLKKLQDKVEKCKQDVLKTKEKY
          ..A.....KKLKE..AAKKAHHT....EK.A...EANSKAD.SLNPEQLKKLQDKVEKCKQDVLKTKEKY
Retrocopy --AAQSLGKKLKE*-AAKKAHHTSVQREK*ASHEEANSKADLSLNPEQLKKLQDKVEKCKQDVLKTKEKY

Parental  EKSLKELDQSTPQYMENMEQVFEQCQQFEEKRLRFFREVLLEVQKHLDLSNVASYKTIYRGLEQSIPGGA
          EKSLKELDQ.TPQYM.NMEQVFEQCQQFEEKRL.F..EVLLEVQKHLDLSNVASYKTIYR.LEQSI...A
Retrocopy EKSLKELDQGTPQYMANMEQVFEQCQQFEEKRLCFW-EVLLEVQKHLDLSNVASYKTIYRDLEQSIRA-A

Parental  EGVEDLKRFRATGEPGWARNWTLAGEWSADLNRTLSRREKKKTADGVTLTGINQTGDQSLQNKPGSNLSV
          ...EDL..FRA...P..A.NW....EWSADLNRTLSRREKK.TADGVTLTGINQTGDQSLQNKP.SNLSV
Retrocopy DAMEDLRWFRANHGPRMAMNWSQFEEWSADLNRTLSRREKK-TADGVTLTGINQTGDQSLQNKPSSNLSV

Parental  PSNPVQSAQSQSSYNPFEDEDDTGSTVSEKEDIKTKNVSSFEKTQSYPTDWSDDESNNPFSSTDANGDSN
          .SNPVQS.QSQSSYNPFEDEDDTGSTVSEKEDIKTKNVSSFEKTQSYPTDWSDDESNNPF.STDANGDSN
Retrocopy LSNPVQSMQSQSSYNPFEDEDDTGSTVSEKEDIKTKNVSSFEKTQSYPTDWSDDESNNPFFSTDANGDSN

Parental  PFDEDTTSGMEVRVRALYDYEGQEHDELSFKAGDELTKMEDEDEQGWCKGRLDSGQVGLYPANYVEAIQ
          P.DEDTTSGMEVRV.ALYDYEGQEHDELS..................CKGR.DSGQVGLYPANYVEAIQ
Retrocopy PLDEDTTSGMEVRVQALYDYEGQEHDELSXXXXXXXXXXXXXXXXXXCKGRSDSGQVGLYPANYVEAIQ

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_262 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_262 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000012990	2 retrocopies	retro_mmur_1629, retro_mmur_262 ,
Rattus norvegicus	ENSRNOG00000009756	2 retrocopies	retro_rnor_1788, retro_rnor_1789,