RetrogeneDB ID: retro_ggor_2511

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:29864861..29865345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSGGOG00000010681
• Aliases: None
• Description: None

Sequence

>retro_ggor_2511
GCAGTAGCAGAGGAACAGAATCCAGAGGATGGAGAAGAGGATGAAGGAGGAGGGAGAACAGTTGGTTCTCATGGAATTAT
CAGGAATTATTGATTCAGACTTTCTCTGGAAATGTGAAAATAAATGCAAAATTTTGAGAACTGACACCAAGAGGCCCTTT
CTGCAAGTGGACAGCTATGTCTTGGCTGGGGAGTCTGAAGACACTCTTGGGACGTGTGTCACATTTGAAGAAAATGTTGA
ACATGTGGATAGAGAGGGCAAGGAGTACACAGTGCTAAAATACAAGTGCCATACAGGGAAGATGTCAGCATGACAAGAAC
TCTTCTGACAGAGAAGGAAGGAGGAGAAAACAGGTGAGGTGGAATGGCTGTAAATCAAGGATAAGGATTTCTCCTCTAGA
CCCAACATGATTTGTAGCTTTCTACATAAAAATGAAGATGAAGAAGTGATAGCTTTGGCCTCAGATAAACCTTTGGAATT
GGAA

Alignment

ORF - retro_ggor_2511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.12 %
• Parental protein coverage: 76.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAADERGPEDGE-DE-EEEEQLVLVELSGIIDSDFLSKCENKCKVLGIDTERPILQVDSCVFAGEYEDTL
          A.A.E..PEDGE.DE.EE.EQLVL.ELSGIIDSDFL.KCENKCK.L..DT.RP.LQVDS.V.AGE.EDTL
Retrocopy AVAEEQNPEDGEEDE>EEGEQLVLMELSGIIDSDFLWKCENKCKILRTDTKRPFLQVDSYVLAGESEDTL

Parental  GTCVIFEENVEHADTEGNNKTVLKYKCHTMKKLSMTRTLLTEKKEGEENIGXXEWLQIKDNDFSYRPNMI
          GTCV.FEENVEH.D.EG...TVLKYKCHT..K.S....L.......EE..G..EWL.IKD.DFS.RPNMI
Retrocopy GTCVTFEENVEHVDREGKEYTVLKYKCHT-GKMSA*QELF*QRRK-EEKTGEVEWL*IKDKDFSSRPNMI

Parental  CNFLHENEDEEVIASAPDKSLELE
          C.FLH.NEDEEVIA.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	0.00 RPM	7.77 RPM
SRP007412_cerebellum	0.00 RPM	8.79 RPM
SRP007412_heart	0.00 RPM	8.29 RPM
SRP007412_kidney	0.00 RPM	22.53 RPM
SRP007412_liver	0.00 RPM	5.22 RPM
SRP007412_testis	0.00 RPM	19.58 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2511 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3714
Pan troglodytes	retro_ptro_2516
Macaca mulatta	retro_mmul_1700
Callithrix jacchus	retro_cjac_3118

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Choloepus hoffmanni	ENSCHOG00000001496	1 retrocopy	retro_chof_1436,
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,
Tupaia belangeri	ENSTBEG00000017031	4 retrocopies	retro_tbel_2653, retro_tbel_3585, retro_tbel_631, retro_tbel_943,