RetrogeneDB ID: retro_ptro_2516

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:28135871..28136355(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSPTRG00000018502
• Aliases: None
• Description: General transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:UniProtKB/TrEMBL;Acc:K7B6B2]

Sequence

>retro_ptro_2516
GCAGTAGCAGAGGAACAGAATCCAGAGGATGGAGAAGAGGATGAAGGAGGAGAGAGAACAGTTGGTTCTCATGGAATTAT
CAGGAATTATTGATTCAGACTTTCTCTCGAAATGTGAAAATAAATGCAAAATTTTGAGAATTGACACCAAGAGGCCCTTT
CTGCAAGTGGACAGCTATGCCTTGGCTGGGGAGTCTGAAGACACTCTTGGGACGTGTGTCACATTTGAAGAAAATGTTGA
ACATGTGGATAGAGAGGGCAAGGAGTACACAGTGCTAAAATACAAGTGCCATACATGGAAGATGTCCGCATGACAAGAAC
TCTTCTGACAGAGAAGGAAGGAGGAGAAAACAGGTGAGGTGGAATGGCTGTAAATCAAGGATAAGGATTTCTCCTCTAGA
CCCAACATGATTTGTAGCTTTCTACATAAAAATGAAGATGAAGAAGTGATAGCTTTGGCCTCAGATAAACCTTTGGAATT
GGAA

Alignment

ORF - retro_ptro_2516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.73 %
• Parental protein coverage: 76.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAADERSPEDGE-DE-EEEEQLVLVELSGIIDSDFLSKCENKCKVLGIDTERPILQVDSCVFAGEYEDTL
          A.A.E..PEDGE.DE.EE.EQLVL.ELSGIIDSDFLSKCENKCK.L.IDT.RP.LQVDS...AGE.EDTL
Retrocopy AVAEEQNPEDGEEDE>EEREQLVLMELSGIIDSDFLSKCENKCKILRIDTKRPFLQVDSYALAGESEDTL

Parental  GTCVIFEENVEHADTEGNNKTVLKYKCHTMKKLSMTRTLLTEKKEGEENIGGVEWLQIKDNDFSYRPNMI
          GTCV.FEENVEH.D.EG...TVLKYKCHT.K..S....L.......EE..G.VEWL.IKD.DFS.RPNMI
Retrocopy GTCVTFEENVEHVDREGKEYTVLKYKCHTWK-MSA*QELF*QRRK-EEKTGEVEWL*IKDKDFSSRPNMI

Parental  CNFLHENEDEEVVASAPDKSLELE
          C.FLH.NEDEEV.A.A.DK.LELE
Retrocopy CSFLHKNEDEEVIALASDKPLELE

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	0.02 RPM	12.96 RPM
SRP007412_cerebellum	0.00 RPM	14.55 RPM
SRP007412_heart	0.00 RPM	40.43 RPM
SRP007412_kidney	0.03 RPM	35.49 RPM
SRP007412_liver	0.00 RPM	22.85 RPM
SRP007412_testis	0.00 RPM	44.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2516 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2516 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3714
Gorilla gorilla	retro_ggor_2511
Macaca mulatta	retro_mmul_1700
Callithrix jacchus	retro_cjac_3118

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118, retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654, retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520, retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237, retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516 , retro_ptro_3145, retro_ptro_3149,