RetrogeneDB ID: retro_ggor_2655

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:48277915..48278597(+)
• Located in intron of: ENSGGOG00000004595

Retrocopy information

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

Parental gene information

• Parental gene symbol: F3
• Ensembl ID: ENSGGOG00000014683
• Aliases: None
• Description: Tissue factor [Source:UniProtKB/TrEMBL;Acc:G3RFF8]

Sequence

>retro_ggor_2655
CTGGCGACTCCAGCCTGGGCCTGGGTCCCACGTCCTGAGACTGCCTTAGCTCAGATGCTCCTGCTCTGCCAGGTCCTCCT
CAAGGCGGCTACTGCTTCTGGCACTGCAGATAGAGTGGTAGCATATAATGTATAATCAACGAATTTCAAGACAGTTTTGG
AGCTGGAACCAAAGCCTATCAATCATGTCTACACTGCTCAGACAAGCTCTGCATCAGGAGACTGGAAAAGCCATGCTTGG
AAACCCTGGACACAGAGAGCAACCTCACAGATGGGACAGCAAGGACGTGACACAGACGTCCTCGGCCCAGGGCCCTTCCT
GCCCCGCTGGGGATGCAGCCACCACGGGTTCTGCCGGGAACCTCTGATCGGAAGCTCCCCAGAGTTTACACGTGACCTGG
AGACACACCTCGGACAGCCAACAATTCAGTGTTTTGAATCAGTCGGGACAAAACAACGTGACAGTATCAGAATGACGTAC
CTTAGAAAGAATGACATATTTCTAGGCCTCTGGAAGTTTGCGACAAGTACTTAAGTTGTACACTTTATTATCGGAAAGCT
TCATGTACGGGAAAGAAAACAGCCAAGACAAACACAAATCCGTTTTTGATGGATATGGATAAAGGGGAAACCACCGTTCC
AATGTTCAAGCAGTGATTCCATCCGAAGACTACACAAGACGA

Alignment

ORF - retro_ggor_2655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.4 %
• Parental protein coverage: 78.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  METPAWSWVPRPETAVARTLLLGWVFAQVAGASGTTNTVAAYNLTWKSTNFKTILEWEPKPINQVYTVQI
          ..TPAW.WVPRPETA.A..LLL..V....A.ASGT...V.AYN....STNFKT.LE.EPKPIN.VYT.Q.
Retrocopy LATPAWAWVPRPETALAQMLLLCQVLLKAATASGTADRVVAYNV--*STNFKTVLELEPKPINHVYTAQT

Parental  STKSGDWKS-KCFYTTDTECDLTDEIV-KDVKQTYLARVFSYPAGNVESTGSAG-EPLYENSPEFTPYLE
          S..SGDWKS..C..T.DTE..LTD....KDV.QT..A...S.PAG....TGSAG.EPL...SPEFT..LE
Retrocopy SSASGDWKS<PCLETLDTESNLTDGTA<KDVTQTSSAQGPSCPAGDAATTGSAG<EPLIGSSPEFTRDLE

Parental  TNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSL-RDVFGKDLIYTLYYWKSSSSGKKTAKTNTNE
          T.LGQPTIQ.FE.VGTK.........T..R.N..FL.L...V..K.L..TLYY.K.S..GKKTAKTNTN.
Retrocopy THLGQPTIQCFESVGTKQRDSI--RMTYLRKNDIFLGL<LEVCDKYLSCTLYYRKASCTGKKTAKTNTNP

Parental  FLIDVDKGE-NYCFSVQAVIPSRTVNRK
          FL.D.DKGE.N....VQAVIPS....R.
Retrocopy FLMDMDKGE<NHRSNVQAVIPSEDYTRR

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	10.93 RPM
SRP007412_cerebellum	0.00 RPM	4.26 RPM
SRP007412_heart	0.00 RPM	7.91 RPM
SRP007412_kidney	0.00 RPM	11.57 RPM
SRP007412_liver	0.00 RPM	11.32 RPM
SRP007412_testis	0.00 RPM	24.97 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_2655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2655 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3952
Pongo abelii	retro_pabe_3256

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117525	1 retrocopy	retro_hsap_3952,
Gorilla gorilla	ENSGGOG00000014683	1 retrocopy	retro_ggor_2655 ,
Nomascus leucogenys	ENSNLEG00000011112	1 retrocopy	retro_nleu_531,
Pongo abelii	ENSPPYG00000001139	2 retrocopies	retro_pabe_3255, retro_pabe_3256,