RetrogeneDB ID: retro_ptro_2182

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:116007444..116008363(+)
• 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_2182
ATGGCATCCATGGGAACCCTCGCCTTTGATGAATATGGGCACCCTTTCCTCATCATCAAGGATCAGGACCACAACTCCTG
TCTTATGGGACTGAGGCCCTTAAGTCTCATATAGTGGCAGAAAAGGCTGTAGCAAATATGATGAGAACATCACTTGGGCC
AAATGGGCTTGATAAGATGATGGTGGATAAGGATGGTGATATGACTGTAACTAACGATGAGTCCCCATCTTAAGCATGAT
GGATGTCGATCATCAGATTGCTAAGCTGATGGCAGAACTGTCCAAGTCTCAGGATGATGAAATTGGACTTGGAACCACAG
GAGTGGTAGTCCTGGCTGCTGCCTTGTTAGAAGAAGCCAAGCAGTTGCTAGACTGAGGCATTCACCCAATCAGAATAGCT
GATGGTTATGAGCAGGCTGCCAGCGTTGCTGTTGAACACCTGGACAAGATCAGTCATAGTGTCCTTGTTGACATAAAGGA
CACTGAACCCCTGATTCCGACTGCAAAAACCATGCTGGGCTCCAAAGTGGTCAAAGTTGGCACCAACAAATGGCTGAGAT
TGCTGTGAATGCTGTCCGCACTGTAGCAGATATGGAGCGGAGAGATATTGACTTTGAGCTCCTCAACGTAGAAGGCAAAG
TGGGCGGGAGGCTGGAGGACACAAAACTGATCAAGGGCGTGATTGTGGACAAGGATTTCCAGTCTCCTATAGGTGCCGAA
AAAAGTGGAAGATGCTAAGATTGCAATTCTCACATGTCCATTTGAACCACCCAAGCCAAAAACAAAGCATAAGCTGGATG
TGACCTCCATAGATCATAAAGCTCTTCACAAATATGAAAAGGAGAAATTTGAAGAGATGATTCAACAAATTAAAGAGACT
GGTGCTAACCTAGCAATTTGTCAGTGGGGCTTTGATGAC

Alignment

ORF - retro_ptro_2182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 56.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASMGTLAFDEYGRPFLIIKDQDRKSRLMGL-EALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVT
          MASMGTLAFDEYG.PFLIIKDQD..S.LMGL.EALKSHI.A.KAVAN.MRTSLGPNGLDKMMVDKDGD.T
Retrocopy MASMGTLAFDEYGHPFLIIKDQDHNSCLMGL<EALKSHIVAEKAVANMMRTSLGPNGLDKMMVDKDGDMT

Parental  VTNDGAT-ILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYE
          VTND....ILSMMDVDHQIAKLM.ELSKSQDDEIG.GTTGVVVLA.ALLEEA.QLLD.GIHPIRIADGYE
Retrocopy VTNDESP<ILSMMDVDHQIAKLMAELSKSQDDEIGLGTTGVVVLAAALLEEAKQLLD*GIHPIRIADGYE

Parental  QAARVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVV-NSCHRQMAEIAVNAVLTVADMERRDVDFE
          QAA.VA.EHLDKIS.SVLVDIKDTEPLI.TAKT.LGSKVV..S.H.QMAEIAVNAV.TVADMERRD.DFE
Retrocopy QAASVAVEHLDKISHSVLVDIKDTEPLIPTAKTMLGSKVV<QSWHQQMAEIAVNAVRTVADMERRDIDFE

Parental  LIKVEGKVGGRLEDTKLIKGVIVDKDFSHPQ-MPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKA
          L..VEGKVGGRLEDTKLIKGVIVDKDF..P...PKKVEDAKIAILTCPFEPPKPKTKHKLDVTS..D.KA
Retrocopy LLNVEGKVGGRLEDTKLIKGVIVDKDFQSPI>VPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSI-DHKA

Parental  LQKYEKEKFEEMIQQIKETGANLAICQWGFDD
          L.KYEKEKFEEMIQQIKETGANLAICQWGFDD
Retrocopy LHKYEKEKFEEMIQQIKETGANLAICQWGFDD

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	0.05 RPM	67.51 RPM
SRP007412_cerebellum	0.04 RPM	66.03 RPM
SRP007412_heart	0.06 RPM	54.91 RPM
SRP007412_kidney	0.03 RPM	86.33 RPM
SRP007412_liver	0.03 RPM	89.79 RPM
SRP007412_testis	0.11 RPM	355.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2182 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2182 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3230
Gorilla gorilla	retro_ggor_2197
Pongo abelii	retro_pabe_2678
Macaca mulatta	retro_mmul_2033

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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,