RetrogeneDB ID: retro_ptro_2133

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:22489229..22490183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSPTRG00000012060
• Aliases: None
• Description: None

Sequence

>retro_ptro_2133
TTGAAGCTTCTTGAAGTTGTCCATCCTGCAGCAAAGACTTCAATGGACATTGCCAAATACCAAGATGCCAAGGTGGGTGA
TAGCACCACCTCAGTGACCTTACTGGCTGCAGAGTTTCTGAAGCAGGTGAAACCTTATGTGGAGGAAGGTTTGCACCCGA
AGATCATCATTCAAGCTTTACGCACAGCCATCCAATTGGCAGTTAATGATAACAAAGAGATCACTGTGACCATGAAGAAG
ACAGAAAAAGTGGAGCAGAAGAAGCTACTTGGAGAAGTGTGCCATCCTGCTCTGAGCTCCAAGCTCATCTCCCAGCAGAA
AGCCTTCTTTGCAAAGATGGTGGTTGATGCAGTGATGATGCTTGATGGTTTGCTGCAGCTTAAAATGATTGGAATCAAGA
AGATACAGGGTGGAGCCCTAGAGGATTCCCATCTGTTACCTGGTGTTTCATTCAAGAATTTCTTTTATGCTGGTGTTGGA
AATGCAACCCCAAAAGTGCTATAATCCCAAGATTTCGCTTTTAAATTTTGAGCTTGAGTTGAAAGTTAGGAAAGATAATG
CTGAGATCAGAGTCCTCACAATGGGGAATTACCAGGCAATTGTTGATGCTGAGTGGAACATTCTCTATGACAAGTTAGCA
AGGATCCATCATTCTGGAGCCAAAGTTGTCTTGTCCAAACTCTCCAATGGGGATGTGGTCACTCAGTACTTTGCTGACAG
GGGCAGGTTCGGTGCTGGCTGAGTACCTGAGAAGGATCTGAATAGGACAATGATGGTCTACAGAGGGTTAATCCAGACCA
TTGTGAATGCTCTGTCAGCAGACATGACATGCTGGGCAGCTAGCTGCCAGGTGTTTGAGGAGACCCTGATTGGAAGTGAG
AGGCACAATTTCTTTACTGGCCTCCCAAGGACAAGACATGCACCTTTATCCTCCACAGTGATGCCACAACTTAT

Alignment

ORF - retro_ptro_2133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 58.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKLLDVVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNK
          LKLL.VVHPAAKT..DIAK.QDA.VGD.TTSVTLLAAEFLKQVKPYVEEGLHP.III.A.RTA.QLAVN.
Retrocopy LKLLEVVHPAAKTSMDIAKYQDAKVGDSTTSVTLLAAEFLKQVKPYVEEGLHPKIIIQALRTAIQLAVND

Parental  IKEIAVTVKKADKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGAL
          .KEI.VT.KK..KVEQ.KLL......ALSSKLISQQKAFFAKMVVDAVMMLD.LLQLKMIGIKK.QGGAL
Retrocopy NKEITVTMKKTEKVEQKKLLGEVCHPALSSKLISQQKAFFAKMVVDAVMMLDGLLQLKMIGIKKIQGGAL

Parental  EDSQLVAGVAFKKTFSYAG-FEMQPKKYHNPKIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNIL
          EDS.L..GV.F.K.F.YAG..EMQP.K..NPKI.LLN.ELELK..KDNAEIRV.T...YQAIVDAEWNIL
Retrocopy EDSHLLPGVSF-KNFFYAG>LEMQPQKCYNPKISLLNFELELKVRKDNAEIRVLTMGNYQAIVDAEWNIL

Parental  YDKLEKIHHSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADV---
          YDKL..IHHSGAKVVLSKL..GDV.TQYFADR..F.AG.VPE.DL.RTMM...G.IQT.VNALSAD....
Retrocopy YDKLARIHHSGAKVVLSKLSNGDVVTQYFADRGRFGAG*VPEKDLNRTMMVYRGLIQTIVNALSADMTCW

Parental  LGRCQVFEETQIGGERYNFFTGC-PKAKTCTFILRGGAEQF
          ...CQVFEET.IG.ER.NFFTG..PK.KTCTFIL...A...
Retrocopy AASCQVFEETLIGSERHNFFTGL<PKDKTCTFILHSDATTY

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	0.04 RPM	111.86 RPM
SRP007412_cerebellum	0.04 RPM	151.64 RPM
SRP007412_heart	0.00 RPM	86.16 RPM
SRP007412_kidney	0.00 RPM	105.65 RPM
SRP007412_liver	0.00 RPM	96.76 RPM
SRP007412_testis	0.00 RPM	527.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2133 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2133 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3354
Gorilla gorilla	retro_ggor_2274
Pongo abelii	retro_pabe_2760
Macaca mulatta	retro_mmul_2093

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133 ,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179, retro_rnor_535,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,