RetrogeneDB ID: retro_tbel_4389

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_80207:2099..3382(-)
• 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_4389
ATGAGAACATCACTGGGACCAAATGGGCTTGACAAGATGATGGATAAGGATGGCGATGTGACCGTGACTAATGACGGTGC
CACCATTCTAAGCATAATGGATGTCGATCACCAGATCGCCAAGCTGATGGTCGAACTATCCAAGTCACAGGATGACGAAA
TCGGAGATGGAACCACAGGGGTGGTTGTCCTGGCTGGTGCCTTGTTGGAAGAAGCTGAGCAGTTGCTGGATCATGGGATC
CACCCCATCAGGATCGCTGACGGCTATGAGCAGGCTGCCCGCATTGCCATGAGCACCTGGACAGGATCAGCGACAGCGTC
CTCATCGACCCCAACGACATCAGGCCCCTGATTCAGACTGCGAAGACCACTCTGGGCTCCAAAGTGGTGAACAGCTGTCA
CTGGCAGATGGCCGAGATCGCCGTGAACACTCTCCTCACTGTTGCAGACATGGAGCGGAGAGATGTGGACTTCGAGCTCA
TCAAAGTGGAAGGCAAAGTGGGCGAGAGGCTGGAGGACATGAAGCTTATCAAGGGCGTAATCGTGGACAAGGATTTCAGC
CACCTGCAGATGCCAAAAAAAGTGAAGGATGCTAAGATTGCAATTCTCACGTGTCCATTTGAACCGCCTAAACCAAAGAC
GAAGCATAAGCTGGATGTGACCTCAGTAGAAGATTATAAAGCCCTTCAGAAATACGAGAAGGAGAAGTTTGAGGAGATGA
TCCAACAAATTAAAGACACAGGCACTAACCTAGCTATCTGCCAGTGGGGCTTTGATGATGAAGTGAATCACTTACTTCTC
CAGAATAACCTGCCTGCAGTCCGCTGCGTAGGAGGCCCTGAAATTGAGTTGATCGCCATTGCAACTGGAGGGCGGATCAT
CCCACGGTTCTCTGAGCTCACAGCTGAGAAGCTGGGCTTCGCTGGGCTCATACAGGAGATCTCATTTGGAACAACTAAAG
ACAAAATGCTGGTCATTGAGAAGTGTAAGAACTCCAGAGACGTCACCATTTTCATTAAAGGAGGAAATAAGATGATTATT
GAAGAAGCAAAACAATCCCTTCATGATGCCCTGTGTGTAATCCGGAACCTGGTCCGTGACAACCGTGTGGTGTACGGAGG
AGGTGCTGCCAAGATAGCGTGCACCTTGGCCGTTAGCCAAGAGACAGGTAAGTGCCCAACCTTGGAGCAGTACACCATGA
GGGCTTTTGCAGACGCGTTGGAGGTCATCCCCATGGTCCTTTCAGAAACAGCGGCATGAACCCCAATCCAAACTATGACC
GAA

Alignment

ORF - retro_tbel_4389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 79.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRTSLGPNGLDKMMVDKDGDVTVTNDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALL
          MRTSLGPNGLDKMM.DKDGDVTVTNDGATILS.MDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALL
Retrocopy MRTSLGPNGLDKMM-DKDGDVTVTNDGATILSIMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALL

Parental  EEAEQLLDRGIHPIRIADGYEQAARIAI-EHLDKISDSVLVDPNDIEPLIQTAKTTLGSKVVNSCHRQMA
          EEAEQLLD.GIHPIRIADGYEQAARIA..EHLD.ISDSVL.DPNDI.PLIQTAKTTLGSKVVNSCH.QMA
Retrocopy EEAEQLLDHGIHPIRIADGYEQAARIAM<EHLDRISDSVLIDPNDIRPLIQTAKTTLGSKVVNSCHWQMA

Parental  EIAVNAVLTVADMERRDVDFELIKVEGKVGGRLEDTKLIKGVIVDKDFSHPQMPKKVEDAKIAILTCPFE
          EIAVN..LTVADMERRDVDFELIKVEGKVG.RLED.KLIKGVIVDKDFSH.QMPKKV.DAKIAILTCPFE
Retrocopy EIAVNTLLTVADMERRDVDFELIKVEGKVGERLEDMKLIKGVIVDKDFSHLQMPKKVKDAKIAILTCPFE

Parental  PPKPKTKHKLDVTSVEDYKALQKYEKEKFEEMIQQIKDTGANLAICQWGFDDEANHLLLQNNLPAVRWVG
          PPKPKTKHKLDVTSVEDYKALQKYEKEKFEEMIQQIKDTG.NLAICQWGFDDE.NHLLLQNNLPAVR.VG
Retrocopy PPKPKTKHKLDVTSVEDYKALQKYEKEKFEEMIQQIKDTGTNLAICQWGFDDEVNHLLLQNNLPAVRCVG

Parental  GPEIELIAIATGGRIVPRFSELTAEKLGFAGLVQEISFGTTKDKMLVIEKCKNSRAVTIFIRGGNKMIIE
          GPEIELIAIATGGRI.PRFSELTAEKLGFAGL.QEISFGTTKDKMLVIEKCKNSR.VTIFI.GGNKMIIE
Retrocopy GPEIELIAIATGGRIIPRFSELTAEKLGFAGLIQEISFGTTKDKMLVIEKCKNSRDVTIFIKGGNKMIIE

Parental  EAKRSLHDALCVIRNLVRDNRVVYGGGAAEIACALAVSQEADKCPTLEQYAMRAFADALEVIPMALSENS
          EAK.SLHDALCVIRNLVRDNRVVYGGGAA.IAC.LAVSQE..KCPTLEQY.MRAFADALEVIPM.LSE..
Retrocopy EAKQSLHDALCVIRNLVRDNRVVYGGGAAKIACTLAVSQETGKCPTLEQYTMRAFADALEVIPMVLSETA

Parental  GMNPIQTMTE
          ...PIQTMTE
Retrocopy A*TPIQTMTE

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_4389 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4389 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.

---

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 ,