RetrogeneDB ID: retro_pabe_1012

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:80385694..80387314(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT5
• Ensembl ID: ENSPPYG00000015342
• Aliases: None
• Description: chaperonin containing TCP1, subunit 5 (epsilon) [Source:HGNC Symbol;Acc:1618]

Sequence

>retro_pabe_1012
GCGTCCATGGGGACCCTCACGTTTGATTGATATGGGCCCCCTTTCCTTATAATCAAAGATCAGGACCGCTAGTCCAGCCT
TATGGGACTTGAGGCCCTCAAGTCTCATATAATGACAGCAAAGGCTTTAGCACATACGACAAGAACATCACTTGGACCAA
AGGGGCTTCATAAGATGATGGTGCATAAGGATGGCAATGTGACTGTAACTAATGATGGGGTCACCATCTTAAGCGTGATG
GATGTCAGTCATCAGATTGCCCAGCTGATGGTAGAAATGTCTAAGTCTCAGGATGATGAAACTGGAGATGGAACCACAGG
TGTGGTTGTCCTGGCTAGTGCCTTGTTAGAAGCAGCCCAGGAGTTGCTAGACCAAGGTATTCATCCAATCAGAATAGCTG
ATGGCTATGAGCAGGCTGCCTGCTTTGCTGTTGAACACCTGGACAAGATCAGTGATAGCATCCTTGTTGACATAAAAAAC
ACCAAACCCCTGATTCAGACTGCAAAAACCATGCTGGGCTCCAAAGTGGTCAACAGTTGTTACCGACAAATGGCTGAGAT
TGCTGTGAATGCCATCCTCCCTTAACAGATATGGAGCAAAGAGGTGTTGACTTTGAGCTTATCAAAGTAGAAAGCAAAGT
GGATGGCAGCCTGGAGGACAATAAACTGATTAAGGGTGTGATTGTGGACAAGGATTTCAGTCACCCACAGATGCCAAAAA
AAGTGGAAGATGCTAAGATTGTAATTCTCACATGTCCACTTGAACTACCCAAACCAAAAGCAAAGCATAAGCTGGATGTG
ACCTCTGTAGAAGATTATAAAGCCCTTCAGAGATATGAAAAGGAGAAATTTTAAGAGATGATTCAACAAATTAAAGAGAC
TGGTGCTAACCCAGAAATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTACTTCTTCAGAACAACTTGCCTGCAG
TTTGCTAGGTAGGAGGACCTGAAATTGAACTGATTGCCATCACAACAAGAGGGCAGATCATCACCAAGTTCTCAGAGCTC
ATGGCCAGGAAGCTGGGCTTTGCTGGTCTTGTACAGGAGATCTCCTTTGGGACAACTAAGGATAAAATGCTGGTCATCAA
GCAGTGTAAGAACTCCAGAGCTATAACCATTTTTATGAGAAGAAGAAATAAGATGATTATTGACGAGGCAAAACAATCCC
TTCACGGTGCTTTGTGTGTCATCTGGAACCTCATCCATAATAATCATGTGGCGTATGGAGGAGGGGCTGCTGAGATATCC
TGTGCTCTGCCAGTTAGCTAAGAGGTGGATAAGTGCCCCACCTTAGAACAGTATGCCATGAGAGCACTTGCCAACACCTT
GGAGGTCATCCCCAAGGCCCTTTCTGAAAACGGTGGCATGAATCCCATCCAGAGTATGACCAAAGTCCGAGCCAGCCAAG
TGAAGGAGATGAACCTTGCTCTTGGCGTCAACTGCTTGCACAAGGGGACAAATGATATGAAGCAATAGCATGTCATAGAA
ACCTTGATTGGCAAAAAAGCAACAGATATCTCTTGCAACACAAATGGTTAGAATGATTTTGAAGACTGACAACATTCATA
AGCCTGGAGAATCTGAAGAA

Alignment

ORF - retro_pabe_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASMGTLAFDEYGRPFLIIKDQDRKSRLMGLEALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVTVT
          ASMGTL.FD.YG.PFLIIKDQDR.S.LMGLEALKSHIM.AKA.A.T.RTSLGP.GL.KMMV.KDG.VTVT
Retrocopy ASMGTLTFD*YGPPFLIIKDQDR*SSLMGLEALKSHIMTAKALAHTTRTSLGPKGLHKMMVHKDGNVTVT

Parental  NDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQAA
          NDG.TILS.MDV.HQIA.LMVE.SKSQDDE.GDGTTGVVVLA.ALLE.A..LLD.GIHPIRIADGYEQAA
Retrocopy NDGVTILSVMDVSHQIAQLMVEMSKSQDDETGDGTTGVVVLASALLEAAQELLDQGIHPIRIADGYEQAA

Parental  RVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVNSCHRQMAEIAVNAVLT-VADMERRDVDFELIK
          ..A.EHLDKISDS.LVDIK.T.PLIQTAKT.LGSKVVNSC.RQMAEIAVNA.L....DME.R.VDFELIK
Retrocopy CFAVEHLDKISDSILVDIKNTKPLIQTAKTMLGSKVVNSCYRQMAEIAVNAILP<LTDMEQRGVDFELIK

Parental  VEGKVGGRLEDTKLIKGVIVDKDFSHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKALQKY
          VE.KV.G.LED.KLIKGVIVDKDFSHPQMPKKVEDAKI.ILTCP.E.PKPK.KHKLDVTSVEDYKALQ.Y
Retrocopy VESKVDGSLEDNKLIKGVIVDKDFSHPQMPKKVEDAKIVILTCPLELPKPKAKHKLDVTSVEDYKALQRY

Parental  EKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVPRFSELTA
          EKEKF.EMIQQIKETGAN..ICQWGFDDEANHLLLQNNLPAV..VGGPEIELIAI.T.G.I...FSEL.A
Retrocopy EKEKF*EMIQQIKETGANPEICQWGFDDEANHLLLQNNLPAVC*VGGPEIELIAITTRGQIITKFSELMA

Parental  EKLGFAGLVQEISFGTTKDKMLVLEQCKNSRASCNHFIRGNKMIIEEAKRSLHDALCVIRNLIRDNRVVY
          .KLGFAGLVQEISFGTTKDKMLV..QCKNSRA......R.NKMII.EAK.SLH.ALCVI.NLI..N.V.Y
Retrocopy RKLGFAGLVQEISFGTTKDKMLVIKQCKNSRAITIFMRRRNKMIIDEAKQSLHGALCVIWNLIHNNHVAY

Parental  GGGAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIPMALSENSGMNPIQTMTEVRARQVKEMNPALG
          GGGAAEISCAL.VS.E.DKCPTLEQYAMRA.A..LEVIP.ALSEN.GMNPIQ.MT.VRA.QVKEMN.ALG
Retrocopy GGGAAEISCALPVS*EVDKCPTLEQYAMRALANTLEVIPKALSENGGMNPIQSMTKVRASQVKEMNLALG

Parental  IDCLHKGTNDMKQQHVIETLIG-KKQQISLATQMVRMILKIDDIRKPGESEE
          ..CLHKGTNDMKQ.HVIETLIG.KKQQISLATQMVRMILK.D.I.KPGESEE
Retrocopy VNCLHKGTNDMKQ*HVIETLIG>KKQQISLATQMVRMILKTDNIHKPGESEE

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	102.90 RPM
SRP007412_cerebellum	0.00 RPM	107.37 RPM
SRP007412_heart	0.03 RPM	63.13 RPM
SRP007412_kidney	0.07 RPM	97.88 RPM
SRP007412_liver	0.03 RPM	87.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1012 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1012 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1219
Pan troglodytes	retro_ptro_834
Macaca mulatta	retro_mmul_1294

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861,
Pongo abelii	ENSPPYG00000015342	2 retrocopies	retro_pabe_1012 , retro_pabe_2678,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618, retro_tbel_4389,