RetrogeneDB ID: retro_mmur_1167

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_2798:77484..78075(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSMICG00000006269
• Aliases: None
• Description: ubiquitin specific peptidase 12 [Source:HGNC Symbol;Acc:20485]

Sequence

>retro_mmur_1167
GCTTCGGCATTAGAGAAAGAGATTGGTCCAGAACAGTTTCCAGTCAATGAGCACTATTTTAGATTAGTCAATTTTGGGAA
TACCTGCTACTGCAGTTCAGTTCTTCAAGCACTTTATTTTTGTCGTCCGTTTCGGGAAAAAGTTCTAGCCTACAAGAGTC
AACCCAGGAAGAAGGAGAACCTTCTTACATGCTTAGCAGATCTCTTCCATAGCATAGCCACTCAGAAGAAAAAGGTTGGA
GTAATACCTCCTAAGAAGTTCATAACAAGGTTACGGAAAGAAAATGAGCTTTTTGACAACTACATGCAACAAGATGCCCA
TGAATTCTTAAATTACCTGCTAAATACAATTGCTGATATTTTACAAGAAGAGAGGAAGCAGGAAAAACAAAGTGGTCGCT
TACCTAATGGTAATATTGATAGTGAAAATAACAACAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTCAGGGAACA
TTAACTAATGAAACCAGATGTCTTACTTGTGAAACTATAAGCAGCAAAGATGAAGATTTTTTAGATCTTTCTGTTGACGT
GGAACAAAACACATCAATTACTCACTGCTTA

Alignment

ORF - retro_mmur_1167 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.97 %
• Parental protein coverage: 55.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKENLLTCLADLFH
          ASALEKEIGPEQFPVNEHYF.LVNFGNTCYC.SVLQALYFCRPFREKVLAYKSQPRKKENLLTCLADLFH
Retrocopy ASALEKEIGPEQFPVNEHYFRLVNFGNTCYCSSVLQALYFCRPFREKVLAYKSQPRKKENLLTCLADLFH

Parental  SIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNGRLPNGNID
          SIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQ.GRLPNGNID
Retrocopy SIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQSGRLPNGNID

Parental  SENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVD-EQNTSITHCL
          SENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVD.EQNTSITHCL
Retrocopy SENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCL

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_1167 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1167 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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167 , retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,