RetrogeneDB ID: retro_ogar_2017

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873580.1:9211742..9212734(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT3
• Ensembl ID: ENSOGAG00000008967
• Aliases: None
• Description: chaperonin containing TCP1, subunit 3 (gamma) [Source:HGNC Symbol;Acc:1616]

Sequence

>retro_ogar_2017
ATGATGGGCCATAGTCCCATACTTGTGCTTAGCCAGAACACAAAGGGTGAATCTGGAAGAGAGTTCAGTCTGGAAACATC
AATGCTGCTAAGACTATTGCAGATATCATCCGAACACATTTGTCCATGATGAAGATGCTTTGGGACCCAATGGGAGGCAT
TGTGATGACCAATGATGGCAATACCATTCTTTGAGAGATTCAAGTCCAGCATCCAGCAGCCAAATCAATGATTGAAATTA
ACCAGATGTAAGATGAAGAAGTTGGAGATGGGACCACATCAGTAATTATTCTTGTGGGGGAAATGTTATCTGTGGCTGAG
CATTTCCTAGAACATCAGATGCATCCAACAGTGGTGATCAGTGCTTACCACAAAGCATTGGATGATATGATCAACACTTT
AAAGAAAATCAGTACCCCTGTTGACATCAATAACCGTGACGTCATGCTGAACATCATTAACAGCTTCGTTACTACCAAAG
CCATCAGCTGGTGGTCTTCTCTGGTGTGCAACATTGCCCTGGATGCTGTCAAGACTGTACAGTATGAGGAGAATGGTCAG
AAGCAGATTGACATCAAAACATATGCAAGGGTGGAAAAGATACCTGGGGGTATCATTGAAGACTCATGTGTCTTCTGTGG
AGTCATGATTAAGAAGGATGTGACCCATCCACGAATGCGGTGCTACATCAAGAACCCTCGGATTGTGCTGTTGGACTCTT
CCCTGGAATACAAGAAAGGGGAAAGCCAGACTGACATTAAGATTACACGAGAGGAAGACTTTACCCGAATCCTCCAGATG
GAAGAAGAGTATATCTAGCAGCTCTGTGAGGACATTATCCAGCTAAAGCCTGATGTGGTCATCACAGAAAAGGGCATCTC
GGATTTAGCTCAGCACTACCTCATGTGGGCCAATATCACAGCCATCTGTAGAGTCCAGAAGACAGACAATAATCACATTG
CTAGAGCCTGGGGGGCCCAGATAGCCGACCAG

Alignment

ORF - retro_ogar_2017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 61.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMGHRPVLVLSQNTKRESGR-KVQSGNINAAKTIADIIRTCLGPKSMMKMLLDPMGGIVMTNDGNAILRE
          MMGH.P.LVLSQNTK.ESGR..VQSGNINAAKTIADIIRT.L...SMMKML.DPMGGIVMTNDGN.IL.E
Retrocopy MMGHSPILVLSQNTKGESGR<RVQSGNINAAKTIADIIRTHL---SMMKMLWDPMGGIVMTNDGNTIL*E

Parental  IQVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAYRKALDDMISTLKK
          IQVQHPAAKSMIEI....DEEVGDGTTSVIIL.GEMLSVAEHFLE.QMHPTVVISAY.KALDDMI.TLKK
Retrocopy IQVQHPAAKSMIEINQM*DEEVGDGTTSVIILVGEMLSVAEHFLEHQMHPTVVISAYHKALDDMINTLKK

Parental  ISTPVDVNNRDVMLNIINSSITTKAISRWSSLACNIALDAVKTVQYEENGRKEIDIKKYARVEKIPGGII
          ISTPVD.NNRDVMLNIINS..TTKAIS.WSSL.CNIALDAVKTVQYEENG.K.IDIK.YARVEKIPGGII
Retrocopy ISTPVDINNRDVMLNIINSFVTTKAISWWSSLVCNIALDAVKTVQYEENGQKQIDIKTYARVEKIPGGII

Parental  EDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIQQLC
          EDSCV..GVMI.KDVTHPRMR.YIKNPRIVLLDSSLEYKKGESQTDI.ITREEDFTRILQMEEEYI.QLC
Retrocopy EDSCVFCGVMIKKDVTHPRMRCYIKNPRIVLLDSSLEYKKGESQTDIKITREEDFTRILQMEEEYI*QLC

Parental  EDIIQLKPDVVITEKGISDLAQHYLMRANITAIRRVRKTDNNRIASRACGARIVSR
          EDIIQLKPDVVITEKGISDLAQHYLM.ANITAI.RV.KTDNN.IA.RA.GA.I...
Retrocopy EDIIQLKPDVVITEKGISDLAQHYLMWANITAICRVQKTDNNHIA-RAWGAQIADQ

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_2017 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005776	1 retrocopy	retro_cjac_1243,
Cavia porcellus	ENSCPOG00000009131	1 retrocopy	retro_cpor_813,
Mus musculus	ENSMUSG00000001416	2 retrocopies	retro_mmus_2352, retro_mmus_824,
Otolemur garnettii	ENSOGAG00000008967	1 retrocopy	retro_ogar_2017 ,
Rattus norvegicus	ENSRNOG00000019090	2 retrocopies	retro_rnor_1450, retro_rnor_2823,
Ictidomys tridecemlineatus	ENSSTOG00000001798	1 retrocopy	retro_itri_788,