RetrogeneDB ID: retro_hsap_3714

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:29591139..29591623(+)
• Located in intron of: ENSG00000223813

Retrocopy information

• Ensembl ID: ENSG00000270196
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSG00000155115
• Aliases: GTF3C6, C6orf51, TFIIIC35, bA397G5.3
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_hsap_3714
GCAGTAGCAGAGGAACAGAATCCAGAGGATGGAGAAGAGGATGAAGGAGGAGGGAGAACAGTTAGTTCTCATGGAATTAT
CAGGAATTATTGATTCAGACTTTCTCTCGAAATGTGAAAATAAATGCAAAATTTTGAGAATTGACACCAAGAGGCCCTTT
CTGCAAGTGGACAGCTATGTCTTGGCTGGGGAGTCTGAAGACACTCTTGGGACGTGTGTCACATTTGAAGAAAATGTTGA
ACATGTGGATAGAGAGGGCAAGGAGTACACAGTGCTAAAATACAAGTGCCATACATGGAAGATGTCAGCATGACAAGAAC
TCTTCTGACAGAGAAGGAAGGAGGAGAAAACAGGTGAGGTGGAATGGCTGTAAATCAAGGATAAGGATTTCTCCTCTAGA
CCCAACATGATTTGTAGCTTTCTACATAAAAATGAAGATGAAGAAGTGATAGCTTTGGCCTCAGATAAACCTTTGGAATT
GGAA

Alignment

ORF - retro_hsap_3714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.34 %
• Parental protein coverage: 76.06 %
• 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.V.AGE.EDTL
Retrocopy AVAEEQNPEDGEEDE>EEGEQLVLMELSGIIDSDFLSKCENKCKILRIDTKRPFLQVDSYVLAGESEDTL

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
bodymap2_adipose	0.00 RPM	34.97 RPM
bodymap2_adrenal	0.00 RPM	50.97 RPM
bodymap2_brain	0.00 RPM	46.55 RPM
bodymap2_breast	0.00 RPM	48.91 RPM
bodymap2_colon	0.08 RPM	44.16 RPM
bodymap2_heart	0.00 RPM	39.95 RPM
bodymap2_kidney	0.00 RPM	56.07 RPM
bodymap2_liver	0.00 RPM	23.57 RPM
bodymap2_lung	0.00 RPM	10.99 RPM
bodymap2_lymph_node	0.00 RPM	23.99 RPM
bodymap2_ovary	0.00 RPM	66.35 RPM
bodymap2_prostate	0.00 RPM	26.72 RPM
bodymap2_skeletal_muscle	0.00 RPM	42.85 RPM
bodymap2_testis	0.00 RPM	77.22 RPM
bodymap2_thyroid	0.00 RPM	47.23 RPM
bodymap2_white_blood_cells	0.00 RPM	26.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3714 was not detected

EST

No EST(s) were mapped for retro_hsap_3714 retrocopy.

TSS

No TSS is located nearby retro_hsap_3714 retrocopy 5' end.

Lab

retro_hsap_3714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3714 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2516
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).