RetrogeneDB ID: retro_ptro_834

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:78892702..78894322(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT5
• Ensembl ID: ENSPTRG00000016725
• Aliases: None
• Description: None

Sequence

>retro_ptro_834
GCGTCCATGGGGACCCTCGCCTTTGATTGATATGGGCCCCCTTTCCTTATCATCAAAGATCAGGACCGCAAGTCCCGCCT
TATGGGACTTGAGGCCCTCAAGTCTCATATAATGGTAGCAAATGCTGTAGCACATGCGACAAGAACATCACTTGGACCAA
AGGGGCTTCATAAGATGATGGTGGATAAGGATGGCGATGTGACTGTAACTAATGATGGGGTCACCATCTTAAGCGTGATG
GATGTCAGTCATCAGATTGCCCAGTTGATGGTGGAAATGTCTAAGTCTCGGGATGATGAAATTGGAGATGGAACCACAGG
TGTGGTTGTCCTGGCTGGTGCCTTGTTAGAAGAAGCCCAGGAGTTGCCAGACCGAAGTATTCATCCAATCAGAATAGCAG
ATGGCTATGAGCAGGCTGCCTGCTTTGCTGTTGAACAACTGGACAAGATCAGTGACAGCATCCTTGTTGACATAAAAGAC
ACCAAACCCCTGATTCAGACTGCAAAAACCACGCTGGGCTCCAAAGTGGTCAACAATTGTTACCGACAAATGGCTGAGAT
TGCTGTGAATGCCATCCTCCCTTAACAGATATGGAGCAGAGAGGTGTTGACTTTGAGCTTATCAAAGTAGAAAGCAAAGT
GGGTGGCAGCCTGGAGGACAATAAACTGATTAAGGGTGTCATTGTGGACAAGTATTTCAGTCACCCACAGATGCCAAAAA
AAGTGGAAGATGCCAAGATTGTAATTCTCACATGTCCATTTGAACTACCCAAACCAAAAGCAAAGCATAAGCTGGATGTG
ACCTCTGTAGAAGATTATAAAGCCCTTTAGAAATATGAAAAGAAGAAATTTTAAGAGATGATTCAACAAATTAAAGAGAC
TGGTGCTAACCTAGAAATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTACTTCTTCAGAACAACTTGCCTGCAG
TTTGCTAGGTAGGAGGACCTGAAATTGAACTGATTGCCATCACAACAGGAGGGCAGATCATCACCAAGTTCTCAGAGCTC
ATGGCCAGGAAGCTGGGCTTTGCTGGTCTTGTACAGGAGATCTCATTTGGGACAACTAAGGATAAAATGCTGGTCATCGA
GCAGTGTAAGAACTCCAGAGCTATAACCATTTTTATGAGAAGAAGAAATAAGATGATTATTGAGGAGGCAAAACAATCCC
TTCACGGTGCTTTGTGTGTCATCTGGAACCTCATCCGTGATAATCATGTGTTGTATGGAGGAGGGGCTGCTGAGATATCC
TGTGCTCTGCCAGTTAGCCAAGAGGTGGATAAGTGTCCCACCTTAGAACAGTATGCCATGAGAGCACTTGCCAACACGTT
GGAGGTCATCCCCAAGGCCCTTTCTGAAAATGGTGGCATGAATTCCATCCAGAGTATGACCAAAGTCCAAGCCAGCCAAG
TGAAGGAGATGAACCTTGCTCTTGGCATCGGCTGTTTGCACAAGGGGACAAATTATATGAAGCAATAGCGTGTCACAGAA
ACCTCGATTGGCAAAAAAGCAACAGATATCTCTTGCAACACAAATGGTTAGAATGATTTTAAAGATTGACAACATTCATA
AGACTGGAGAATCTGAAGAA

Alignment

ORF - retro_ptro_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.13 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASMGTLAFDEYGRPFLIIKDQDRKSRLMGLEALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVTVT
          ASMGTLAFD.YG.PFLIIKDQDRKSRLMGLEALKSHIM.A.AVA...RTSLGP.GL.KMMVDKDGDVTVT
Retrocopy ASMGTLAFD*YGPPFLIIKDQDRKSRLMGLEALKSHIMVANAVAHATRTSLGPKGLHKMMVDKDGDVTVT

Parental  NDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQAA
          NDG.TILS.MDV.HQIA.LMVE.SKS.DDEIGDGTTGVVVLAGALLEEA..L.DR.IHPIRIADGYEQAA
Retrocopy NDGVTILSVMDVSHQIAQLMVEMSKSRDDEIGDGTTGVVVLAGALLEEAQELPDRSIHPIRIADGYEQAA

Parental  RVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVNSCHRQMAEIAVNAVLT-VADMERRDVDFELIK
          ..A.E.LDKISDS.LVDIKDT.PLIQTAKTTLGSKVVN.C.RQMAEIAVNA.L....DME.R.VDFELIK
Retrocopy CFAVEQLDKISDSILVDIKDTKPLIQTAKTTLGSKVVNNCYRQMAEIAVNAILP<LTDMEQRGVDFELIK

Parental  VEGKVGGRLEDTKLIKGVIVDKDFSHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKALQKY
          VE.KVGG.LED.KLIKGVIVDK.FSHPQMPKKVEDAKI.ILTCPFE.PKPK.KHKLDVTSVEDYKAL.KY
Retrocopy VESKVGGSLEDNKLIKGVIVDKYFSHPQMPKKVEDAKIVILTCPFELPKPKAKHKLDVTSVEDYKAL*KY

Parental  EKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVPRFSELTA
          EK.KF.EMIQQIKETGANL.ICQWGFDDEANHLLLQNNLPAV..VGGPEIELIAI.TGG.I...FSEL.A
Retrocopy EKKKF*EMIQQIKETGANLEICQWGFDDEANHLLLQNNLPAVC*VGGPEIELIAITTGGQIITKFSELMA

Parental  EKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIRDNRVVY
          .KLGFAGLVQEISFGTTKDKMLVIEQCKNSRA.TIF.R..NKMIIEEAK.SLH.ALCVI.NLIRDN.V.Y
Retrocopy RKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAITIFMRRRNKMIIEEAKQSLHGALCVIWNLIRDNHVLY

Parental  GGGAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIPMALSENSGMNPIQTMTEVRARQVKEMNPALG
          GGGAAEISCAL.VSQE.DKCPTLEQYAMRA.A..LEVIP.ALSEN.GMN.IQ.MT.V.A.QVKEMN.ALG
Retrocopy GGGAAEISCALPVSQEVDKCPTLEQYAMRALANTLEVIPKALSENGGMNSIQSMTKVQASQVKEMNLALG

Parental  IDCLHKGTNDMKQQHVIETLIG-KKQQISLATQMVRMILKIDDIRKPGESEE
          I.CLHKGTN.MKQ..V.ET.IG.KKQQISLATQMVRMILKID.I.K.GESEE
Retrocopy IGCLHKGTNYMKQ*RVTETSIG>KKQQISLATQMVRMILKIDNIHKTGESEE

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	0.00 RPM	67.51 RPM
SRP007412_cerebellum	0.00 RPM	66.03 RPM
SRP007412_heart	0.00 RPM	54.91 RPM
SRP007412_kidney	0.00 RPM	86.33 RPM
SRP007412_liver	0.03 RPM	89.79 RPM
SRP007412_testis	0.00 RPM	355.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_834 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_834 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1219
Pongo abelii	retro_pabe_1012
Macaca mulatta	retro_mmul_1294

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 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,
Pan troglodytes	ENSPTRG00000016725	2 retrocopies	retro_ptro_2182, retro_ptro_834 ,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618, retro_tbel_4389,