RetrogeneDB ID: retro_pabe_2678

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:116561567..116562957(+)
• 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_2678
ATCTTAAGCATGATGGATGTCGATCATCAAATTGCTAAGCTGATGGCGGAACTGTCCAAGTCTCAGGATGATGAAATTGG
ACTTGGAACCACAGGAGTGGTAGTCCTGGCTGCTGCCTTGTTACAAGAAGCCAAGCAGTTGCTAGACTGAGGCATTCACC
CAATCAGAATAGCTGATGGTTATGAGCAGGCTGTCAGCGTTGCTGTTGAACACCTGGACAAGATCAGTCATAGTGTCCTT
GTCGACATAAAGGACACTGAACCCCTGATTCCAACTGCAAAAACCATGCTGGGCTCCAAAGTGGTCAAAGTTGGCACCAA
CAAATGGCTGAGATTGCTGTGAATGCTGTCCTCACTGTAGCAGATATGGAGCGGAGAGATACTGACTTTGAGCTCGTCAA
CGTAGAAGGCAAAGTGGGCGGGAGGCTGGAGGACAGAAAACTGATTAAGGGCGTGATTGTGGACAAGGATTTCCAGTCAC
CTATAGGTGCTGAAAAAAGTGGAAGATGCCAAGATTGCAATTCTCACATGTCCATTTGAACCACCGAAGCCAAAAAACAA
AGCATAAGCTGGATGTGACCTCCATAGATCATAAAGCTCTTCAGAAATATGAAAAGGAGAAATTTGAAGAGATGATTCAA
AAAATTAAACAGACTGGTGCTAACCTAGCAATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTATTTCTTCAGAA
CAACTTGCCTGTGGTTCGCTGGGTAGGGGGACTTGAAATTGAACTTATTGCCATCTCAACAAAAGGGCGGATTGTCCCAG
GTTCTCAGAGCTCATGGGCGAGACGCTGGGCTTTACCGGTCTTGTACAGGAGATCTCATTTGGGACAACTAAGGATAAAA
TGCTGGTCATCGAGCAGTGTAAGAACTCCAGAGCTGTAACCATTTTTATTAGAGGAGGAAATAAGATGATCATTGAGGAG
GTGAAACGATCCCTTCACGATGCTTTGTGTGTCATCAGCAACCTCATCCGCAATAATTGTGTGGCATACGGAGGAGGGTT
TGCTGAGATATCCTGTGCTCTGGCAGTTAGCCAAGAGGTGGATAAGCGCCCCACCTTAGACCAGTACACCACAAGAGCGT
TTGCCAACGCTCTGGAGTTGCCCCATGGGCCTTTTTGAAAACAGTGGCATGAATCCCATCCAGACTATGACAAAAGTCCG
AGCCAGACAAGTGAAAGATATGAACCCTGCTCTCGGTACTGACTGTTTCCACAAGGGGACAAATGATATGAAGCAACAGC
ATGTCATAGAAATCTTAATTGGCAAAAAGCAACAGACATCTTTCACAACACAAATGGTTAGAATGATTGTGAAGATTGAT
GACATTCATAAGCCTGGAGAATCTGAAGAA

Alignment

ORF - retro_pabe_2678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 85.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQAARVAIE
          ILSMMDVDHQIAKLM.ELSKSQDDEIG.GTTGVVVLA.ALL.EA.QLLD.GIHPIRIADGYEQA..VA.E
Retrocopy ILSMMDVDHQIAKLMAELSKSQDDEIGLGTTGVVVLAAALLQEAKQLLD*GIHPIRIADGYEQAVSVAVE

Parental  HLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVN-SCHRQMAEIAVNAVLTVADMERRDVDFELIKVEGKV
          HLDKIS.SVLVDIKDTEPLI.TAKT.LGSKVV..S.H.QMAEIAVNAVLTVADMERRD.DFEL..VEGKV
Retrocopy HLDKISHSVLVDIKDTEPLIPTAKTMLGSKVVK<SWHQQMAEIAVNAVLTVADMERRDTDFELVNVEGKV

Parental  GGRLEDTKLIKGVIVDKDF-SHPQMPKKVEDAKIAILTCPFEPPKPK-TKHKLDVTSVEDYKALQKYEKE
          GGRLED.KLIKGVIVDKDF.SH....KKVEDAKIAILTCPFEPPKPK.TKHKLDVTS..D.KALQKYEKE
Retrocopy GGRLEDRKLIKGVIVDKDF>SHL*VLKKVEDAKIAILTCPFEPPKPK>TKHKLDVTSI-DHKALQKYEKE

Parental  KFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVP-RFSELTAEK
          KFEEMIQ.IK.TGANLAICQWGFDDEANHL.LQNNLP.VRWVGG.EIELIAI.T.GRIVP.RFSEL..E.
Retrocopy KFEEMIQKIKQTGANLAICQWGFDDEANHLFLQNNLPVVRWVGGLEIELIAISTKGRIVP<RFSELMGET

Parental  LGFAGLVQEISFGTTKDKMLVLEQCKNSRASCNHFIRGNKMIIEEAKRSLHDALCVIRNLIRDNRVVYGG
          LGF.GLVQEISFGTTKDKMLV.EQCKNSRA.......GNKMIIEE.KRSLHDALCVI.NLIR.N.V.YGG
Retrocopy LGFTGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEVKRSLHDALCVISNLIRNNCVAYGG

Parental  GAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIP-MALSENSGMNPIQTMTEVRARQVKEMNPALGI
          G.AEISCALAVSQE.DK.PTL.QY..RAFA.ALE..P.M.L.ENSGMNPIQTMT.VRARQVK.MNPALG.
Retrocopy GFAEISCALAVSQEVDKRPTLDQYTTRAFANALE-LP>MGLFENSGMNPIQTMTKVRARQVKDMNPALGT

Parental  DCLHKGTNDMKQQHVIETLIGKKQQISLATQMVRMILKIDDIRKPGESEE
          DC.HKGTNDMKQQHVIE.LIGKKQQ.S..TQMVRMI.KIDDI.KPGESEE
Retrocopy DCFHKGTNDMKQQHVIEILIGKKQQTSFTTQMVRMIVKIDDIHKPGESEE

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	6.14 RPM	102.90 RPM
SRP007412_cerebellum	8.63 RPM	107.37 RPM
SRP007412_heart	4.67 RPM	63.13 RPM
SRP007412_kidney	5.80 RPM	97.88 RPM
SRP007412_liver	5.60 RPM	87.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2678 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2678 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3230
Pan troglodytes	retro_ptro_2182
Gorilla gorilla	retro_ggor_2197
Macaca mulatta	retro_mmul_2033

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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,