RetrogeneDB ID: retro_pabe_2760

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:93468195..93469291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSPPYG00000012297
• Aliases: None
• Description: T-complex protein 1 subunit eta [Source:RefSeq peptide;Acc:NP_001126797]

Sequence

>retro_pabe_2760
TTGAAGCTTCTTGAAGTTGTCCATCCTGCAGCAAAGACTTCGATGGACATTGCCAAATATCAAGATGCCGAGGTGGGTGA
TGGCACCACCTCAGTGACCTTGCTAGCTGCAGAGTTTCTGAAGCAGGTGAAACCTTATGTGGAGGAAGGTTTGCACCCAA
AGATCATCATTCAAGCTTTATGCACAGCCATCCAATTGGCAGTTAATGATAACAAAGAGATCACTGCGACCATGAAGAAG
ACAGAAAAAGTGGAGCAGAAGAAGCTGCTTGGAGAAGTGTGCCATCCTGCTCTGAACTCCAAGCTCATCTCCCAGCAGAA
AGCCTTCTTTGCAAAGATGGTGGTTGATGCAGTGATGATGCTTGATGGTTTGCTGCAGCTTAAAATGATTGGAATCAAGA
AGATACAGGGTGGAGCCCTAGAGGATTCCCATCTGTTAGCTGGTGTTGCACTCAAGAATTTCTTTTATGCTGGGTTGGAA
ATGCAACCCCTAAAGTGCCATGATCCCAAGATTGAACTTTTAAATTTTGAGCTTGATTTGAAAGTTAAGAAAGATAATGC
TGAGATCAGAGTCCTCACAATGGGGAATTACCAGGCAATTGTTGATGCTGAGTGGAACATTCTCTATGACAAGTTAGCAA
GGATCCATCATTCTGGAGCCAAAGTTGTTTTGTCCAAACTCTCCAATGGGGATGTGGTCACTCAGTACTTTGCTGACAGG
GGCAGGTTTGGTGCTGGCCGATTACCTGAAAAGGATCTGAATAGGACAATGATGGCCTACAGAGGGTCGATCCAGACCAT
TGTGAATGCTCTGTCAGCAGACATGCTGGGCAGCTGCCAGGTGTTTGAGGAGACCCTGACTGGAAGTGAGAGGCACAATT
TCTTTACTGGCCTCCCAAGGCCAAGACATGCACCTTTATCCTCCACAGTGATGCCACAACTTTGGAGGAGACAGAACAGT
TCATGCCTAATGCCATCATGATTTTCAGGAGGGCCATTGAAAATGATTTGGTGGTGGCTGGTGGTGGGGCCATTCAGATA
AAGCTCTCCAAGTACCTATGAGATTAGCAAGGACTATTCCAGGAACACAGCAGCTA

Alignment

ORF - retro_pabe_2760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 67.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKLLDVVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNK
          LKLL.VVHPAAKT..DIAK.QDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHP.III.A..TA.QLAVN.
Retrocopy LKLLEVVHPAAKTSMDIAKYQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPKIIIQALCTAIQLAVND

Parental  IKEIAVTVKKADKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGAL
          .KEI..T.KK..KVEQ.KLL......AL.SKLISQQKAFFAKMVVDAVMMLD.LLQLKMIGIKK.QGGAL
Retrocopy NKEITATMKKTEKVEQKKLLGEVCHPALNSKLISQQKAFFAKMVVDAVMMLDGLLQLKMIGIKKIQGGAL

Parental  EDSQLVAGVAFKKTFSYAGFEMQPKKYHNPKIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILY
          EDS.L.AGVA..K.F.YAG.EMQP.K.H.PKI.LLN.EL.LK..KDNAEIRV.T...YQAIVDAEWNILY
Retrocopy EDSHLLAGVAL-KNFFYAGLEMQPLKCHDPKIELLNFELDLKVKKDNAEIRVLTMGNYQAIVDAEWNILY

Parental  DKLEKIHHSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRC
          DKL..IHHSGAKVVLSKL..GDV.TQYFADR..F.AGR.PE.DL.RTMMA..GSIQT.VNALSAD.LG.C
Retrocopy DKLARIHHSGAKVVLSKLSNGDVVTQYFADRGRFGAGRLPEKDLNRTMMAYRGSIQTIVNALSADMLGSC

Parental  QVFEETQIGGERYNFFTGC-PKAKTCTFILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEM
          QVFEET..G.ER.NFFTG..PKAKTCTFIL...A....EETE.....AIMI.RRAI.ND.VVAGGGAI..
Retrocopy QVFEETLTGSERHNFFTGL<PKAKTCTFILHSDATT-LEETEQFMPNAIMIFRRAIENDLVVAGGGAIQI

Parental  ELSKYLRD-YSRTIPGKQQL
          .LSKYL.D...RTIPG.QQL
Retrocopy KLSKYL*D<LARTIPGTQQL

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	111.96 RPM
SRP007412_cerebellum	0.49 RPM	145.68 RPM
SRP007412_heart	0.06 RPM	55.09 RPM
SRP007412_kidney	0.03 RPM	71.07 RPM
SRP007412_liver	0.00 RPM	53.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2760 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2760 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3354
Pan troglodytes	retro_ptro_2133
Gorilla gorilla	retro_ggor_2274
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,