RetrogeneDB ID: retro_tbel_1618

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_526:62744..63618(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT5
• Ensembl ID: ENSTBEG00000001201
• Aliases: None
• Description: chaperonin containing TCP1, subunit 5 (epsilon) [Source:HGNC Symbol;Acc:1618]

Sequence

>retro_tbel_1618
ATTATGATTCTCACATGTCCATTTGTCTGCCTAAACCAAAGACGAAGCATAAGCTGGATGTGACCTTTGTAAAAGATTAT
AAAGCCCTTCAGAAATATGAAAAGGAGAAATTTGAAGAGATGATCCAACAAATTAAAGACTGGGGTGCTAACCTAGTTAT
TTGCCAATGGGGCTTTGATTATAAAACAAATTATTTACTTCAGAATAACCTATCTGTGGTCTGCAGGGTAGAGAGACCTG
AAATTGGGCTGATCACCATTACAACAGGAAAGCAGATATCCCATGGTTCTCTGAGCTCAGAGCTGAGAATCTGGGCTTTG
CTAGGCTTGGACAGGAGATCTCATTTGGGACAACTAAAGACAAAATGCTAGTCATTGAGAAGTGTAAGAACTCCAGAACT
GTCACCATTCTCATTAGAGGAGGAACGAAGATGATCATCGAAGAAACAAAATAATCCCTTCGTGATGCTTCGTATGTCAT
CCGGAATCTTGTCTGTGCCAATTGTGTGGTGTATGGAGGAGGTGCTGTTGAAATATCTGTGCTTTGTCCATTAGTCAAGA
GACAGATAAGTGCCCAACCTTGGAGCAATATGCCGTGAGAGCTTTGAAGATGGATTGGAGTTCAGCCCCATGGCTCTTTC
TAGAAACAGTGGCATGAATCCCATCCAGACTGTAACTGAAATCCAAACCAGACAAGTGAAGGAGATGAACCTTGTTCTTG
GAATTGACTGTTTTCATAAGGTTACAAATAATATGAAGCAACAACATGTCATAGAAACCTTGATTGGCAAAAAGCAACAG
ATATCATTTGCAACAAAAATGGTCAGAATGATTTTGAAGATGATAATATCCATAAACCTGGAGAATATGAAGAA

Alignment

ORF - retro_tbel_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.25 %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IAILTCPFEP-PKPKTKHKLDVTSVEDYKALQKYEKEKFEEMIQQIKDTGANLAICQWGFDDEANHLLLQ
          I.ILTCPF...PKPKTKHKLDVT.V.DYKALQKYEKEKFEEMIQQIKD.GANL.ICQWGFD...N.LL.Q
Retrocopy IMILTCPFVC<PKPKTKHKLDVTFVKDYKALQKYEKEKFEEMIQQIKDWGANLVICQWGFDYKTNYLL-Q

Parental  NNLPAVRWVGGPEIELIAIATGGRI-VPRFSELTAEKLGFAGLVQEISFGTTKDKMLVIEKCKNSRAVTI
          NNL..V..V..PEI.LI.I.TG..I..P.FSEL.AE.LGFA.L.QEISFGTTKDKMLVIEKCKNSR.VTI
Retrocopy NNLSVVCRVERPEIGLITITTGKQI<IPWFSELRAENLGFARLGQEISFGTTKDKMLVIEKCKNSRTVTI

Parental  FIRGGNKMIIEEAKRSLHDALCVIRNLVRDNRVVYGGGAAEIA-CALAVSQEADKCPTLEQYAMRA-FAD
          .IRGG.KMIIEE.K.SL.DA..VIRNLV..N.VVYGGGA.EI..CAL..SQE.DKCPTLEQYA.RA.F.D
Retrocopy LIRGGTKMIIEETK*SLRDASYVIRNLVCANCVVYGGGAVEIS<CALSISQETDKCPTLEQYAVRA<FED

Parental  ALEVIPMALSENSGMNPIQTMTEVRARQVKEMNPALGIDCLHKGTNDMKQQHVIETLIGKKQQISLATQM
          .LE..PMALS.NSGMNPIQT.TE...RQVKEMN..LGIDC.HK.TN.MKQQHVIETLIGKKQQIS.AT.M
Retrocopy GLEFSPMALSRNSGMNPIQTVTEIQTRQVKEMNLVLGIDCFHKVTNNMKQQHVIETLIGKKQQISFATKM

Parental  VRMILKI-DDIRKPGESEE
          VRMILK..D.I.KPGE.EE
Retrocopy VRMILKM<DNIHKPGEYEE

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1618 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1618 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008977	1 retrocopy	retro_cjac_516,
Homo sapiens	ENSG00000150753	2 retrocopies	retro_hsap_1219, retro_hsap_3230,
Gorilla gorilla	ENSGGOG00000024064	1 retrocopy	retro_ggor_2197,
Macaca mulatta	ENSMMUG00000020112	2 retrocopies	retro_mmul_1294, retro_mmul_2033,
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861,
Pongo abelii	ENSPPYG00000015342	2 retrocopies	retro_pabe_1012, retro_pabe_2678,
Pan troglodytes	ENSPTRG00000016725	2 retrocopies	retro_ptro_2182, retro_ptro_834,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618 , retro_tbel_4389,