RetrogeneDB ID: retro_itri_788

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393322.1:2850704..2851815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT3
• Ensembl ID: ENSSTOG00000001798
• Aliases: None
• Description: chaperonin containing TCP1, subunit 3 (gamma) [Source:HGNC Symbol;Acc:1616]

Sequence

>retro_itri_788
AATATCATCCTGGATGCTGTCAAAACTGTACAGTTTGAGGAAAAGGATCAGAAGGAGATTGACATCAAGAAATATGCAAG
AGTGGAAAAAGATACTTGGGAGCATCATTGAAGACTCATGTGTATTACATGGAGTCATGATTAACAAAGATGTGACCTAT
CTGAAAATATGGCATTATATGAAGAACCCTCATATTGGGCTATTGGATTCTTCTCTGGAATACAGAAAGGAGAAAGCCAG
ACTGACATTGAGATTACCCAAGAGGAAGACTTCACCTGAATTCTCCAAATGGAAAAAAAAGAGTATATCCAGCATCTCTG
TGAGGACATTATTCAACTGAAGTCTGATGTGGTCATCACAGAAAAAAGGCATCTCAGACTTAGCTCAGCACTACCTCATG
CGGGCCAATATCTCAGCCATCTGCAGAGTCCAGAGGACAGACAATAATTGCATTGCTAGAGCATGCAGGGCCCAGATAGT
CAGCTGACCAGAAGAACTGAGAGAAGATGATGTTGGAACAGGGGCAAACCTGTTGGAAATCAAGAAAATTGGAGATGAGT
ACTTTAGGTTCATCAGTGAGCGCAGAGACCCCAAGGCCTACACCATTCTTCTCAGGGAGGCCAACAAAGAAATTCTCTCA
GATGAAGATCGCAACCTTCAGGATGCCATGTAAGTGTGCTGAAATGTTCTCCTGGACGCTTAGCTGGTGCCAGGGGATGG
GGCTTCTGAGGTGGCTGTAGCTCACCCCTTAACAGAAAAATCCATGGCCATGATTGGTGTGGAACAATGGTGATACAGGG
CTATTTCCCAGACTTTAGAAGTCATCCCTCATACCTTGATCCAGAATTGTGGGGCCAGCATTATAAATCTACTCACTTCC
CTTTGGGCCAAGCACACCCAGGAGACCTGGGAAGTAAGTGGTGAGATGGGAACTTTAGTGGACATGAAAGAACTAGGCAT
ATGGAAGCCATTGGCTGTGAAGCTGCAAACATATAAGGCAGCAGTGGAGATGGCAATTCTCCTACTGTGGATAGATGACA
TCATATCAGACCACAAAAAGAAGGGTGATGACCAGAGCCGGAAAGGAGGGGCTCCTGATGCTGGCCAGGAA

Alignment

ORF - retro_itri_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NIALDAVKTVQFEENGRKEIDIKKYARVEK-IPGGIIEDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLD
          NI.LDAVKTVQFEE...KEIDIKKYARVEK.I.G.IIEDSCVL.GVMINKDVT......Y.KNP.I.LLD
Retrocopy NIILDAVKTVQFEEKDQKEIDIKKYARVEK>ILGSIIEDSCVLHGVMINKDVTYLKIWHYMKNPHIGLLD

Parental  SSLEYKK-GESQTDIEITREEDFTRILQMEE-EYIQQLCEDIIQVKPDVVITE-KGISDLAQHYLMRANI
          SSLEY.K.GESQTDIEIT.EEDFT.ILQM...EYIQ.LCEDIIQ.K.DVVITE.KGISDLAQHYLMRANI
Retrocopy SSLEYRK<GESQTDIEITQEEDFT*ILQMXXXEYIQHLCEDIIQLKSDVVITE>KGISDLAQHYLMRANI

Parental  TAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITECKDPKACTILLRGA
          .AI.RV..TDNN.IARAC.A.IVS.PEELREDDVGTGA.LLEIKKIGDEYF.FI.E..DPKA.TILLR.A
Retrocopy SAICRVQRTDNNCIARACRAQIVS*PEELREDDVGTGANLLEIKKIGDEYFRFISERRDPKAYTILLREA

Parental  SKEILSEVERNLQDAMQVCRNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPR
          .KEILS...RNLQDAM.VC.NVLLD..LVPG.GASE.AVAH.LTEKS.AM.GVEQW.YRA..Q.LEVIP.
Retrocopy NKEILSDEDRNLQDAM*VC*NVLLDA*LVPGDGASEVAVAHPLTEKSMAMIGVEQW*YRAISQTLEVIPH

Parental  TLIQNCGASMIRQLTSLRAKHTQENCETWGVNGETGTLVDMKELGIWEPLAVKLQTYKTAVETAVLLLRI
          TLIQNCGAS.I..LTSL.AKHTQE...TW.V.GE.GTLVDMKELGIW.PLAVKLQTYK.AVE.A.LLL.I
Retrocopy TLIQNCGASIINLLTSLWAKHTQE---TWEVSGEMGTLVDMKELGIWKPLAVKLQTYKAAVEMAILLLWI

Parental  DDIVSGHKKKGDDQSRQGGAPDAGQE
          DDI.S.HKKKGDDQSR.GGAPDAGQE
Retrocopy DDIISDHKKKGDDQSRKGGAPDAGQE

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_788 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_788 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 ,