RetrogeneDB ID: retro_ogar_2897

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873677.1:155386..156207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSOGAG00000030639
• Aliases: None
• Description: ubiquitin specific peptidase 12 [Source:HGNC Symbol;Acc:20485]

Sequence

>retro_ogar_2897
GGAGCCAATGCTTCGGCATTAGAGAAAGAGATTGGACCAGAACAGTTTCCAGCCAATGCGCACTATTTTGGATTAGTCAA
TTTGGGGAATACCCACTACAGTCATTCAGTTCTTAAGCACTTTTATCTTTGTTATCCATTTCTGGAAAAAGTTCTAGCCT
GCAAAAGTCAACCTAGGAAGGAGAACCTTCCTACATGCTTGGCAGATCGCTTCCGTAGCACAGCCACCCAGAAGAAAAAG
GTTGGAGTAATACCTCCAAAGAAGTTCGTAACAAGGTTATGGAAAGAAAAAGAGGTTTTTGACAACTACATGCAACAAGA
TGCTCATGAATTCTTAAATTACCTACTAAATACAATTGCTGATATTTTACAAGAAGAGAGAAATCAAGAAAAACAAAATG
GTCATTTACCCAATGGTAATATTGATAGTGAAAATAATAACAGCCCACCAGACCCACCATGGGTTCATGGGATTGTTCAG
GGAACATTAACTAATGAAACCAGAAGTCTTACTTGTGAAACTATAAGCAGCAATGGTGAAGATTTTTTAGATCATTCTGT
TGACTGGAACAAAACACATCAATTACTCACTGTTTAAGGGGTTCTAGCAACTCAGAAACTCTACGCAGTAAATACTAATA
CTACTGTGATGAGTGTGACAGCAAACAGGAAGCACACAAACGGATGGAAGTTCAAAAACGGCCCATGATTCTAGCTCTAC
AACGGAAGAGATTTTAATGTATGGATCAGCTTTATGGATATACAAATCTTTCTTACCGGGTAGTTTTTCCTTTAGAACTT
TTTCTATTGAGCCAGGTGGGT

Alignment

ORF - retro_ogar_2897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.71 %
• Parental protein coverage: 74.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKENLLTCLAD
          GANASALEKEIGPEQFP.N.HYFGLVN.GNT.Y..SVL...Y.C.PF.EKVLA.KSQPRK.ENL.TCLAD
Retrocopy GANASALEKEIGPEQFPANAHYFGLVNLGNTHYSHSVLKHFYLCYPFLEKVLACKSQPRK-ENLPTCLAD

Parental  LFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNGRLPNG
          .F.S.ATQKKKVGVIPPKKF.TRL.KE.E.FDNYMQQDAHEFLNYLLNTIADILQEER.QEKQNG.LPNG
Retrocopy RFRSTATQKKKVGVIPPKKFVTRLWKEKEVFDNYMQQDAHEFLNYLLNTIADILQEERNQEKQNGHLPNG

Parental  NIDSENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVD-VEQNTSITHCLRGFSNTETL
          NIDSENNNS.PDP.WVH.I.QGTLTNETR.LTCETISS..EDFLD.SVD..EQNTSITHCLRG.SN.ETL
Retrocopy NIDSENNNSPPDPPWVHGIVQGTLTNETRSLTCETISSNGEDFLDHSVD<LEQNTSITHCLRGSSNSETL

Parental  CSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLFNTSG
          .S.Y.YYC.EC.SKQEAHKRM.V.K.PMILAL..KRF..MDQL..YT.LSYRVVFPLEL.L....G
Retrocopy RSKY*YYCDECDSKQEAHKRMEVQKRPMILALQRKRF*CMDQLYGYTNLSYRVVFPLELFLLSQVG

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2897 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 10 parental genes, and 25 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	ENSOGAG00000009357	1 retrocopy	retro_ogar_3339,
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,