RetrogeneDB ID: retro_ggor_2770

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:5125222..5126358(+)
• Located in intron of: ENSGGOG00000007243

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCF3
• Ensembl ID: ENSGGOG00000003667
• Aliases: None
• Description: None

Sequence

>retro_ggor_2770
GGGGTCTATTCCTCCTTTGGTAGAGACGCAGGCGTGCGCAGCCTGACTCAGGCTGGCTTCCTGCCGGGCAAGCTGGCCCT
CAGCAGCCCCGGACCTCTGTCCCCTTCAGGCATGAAGGGGACCTCCCAGTACTACCCCTCCTACGCCAGCAGCTCTGGCG
GACAGAGGCGGACAGCGGCCTGGACACGCAGCCCACGAAGGTCGGGAATGTCCCGCCTGGTCTTCCATCCTTGGCGTACC
TGCCCAGCTCAGGTGAGGAGTACGGTAGGGATGCCGCCGCCTATCCATCCGCCAAGACGCCCAGCAGCGCCTGTCCCGCC
CCCTTCTACATGGCAGATGGCAGCCTGCACCCCTAAGCTGAGCTCTGGAGTTCCCCGGGCCAGGTGGGCTTTGGCCCCAT
GCTGGGCGGGGGCTCATCCCCCTCGTCCCTCCCGCCCGGCAGCGGCCCTGTGGGCAGTGGCGGAGGCAGCAGCACGTTTG
GCGGCCTGCACCAGCACGAGCGCATGGGCTACCAGCTGCACGGAGCAGAAGTGAACGGTGGGCTTCTGGCTGCATCCACC
TTCTCCTTGGCCCCCGGAGCCACGTACGGCGGCGTATCCAGCCACACGCCTGTCAGCGGGGCCGACAACCTCCTGGGCTC
CCGAGGGACCACAGCCAGCAGCTCTGGGGACGCCCTCGGGAAGGCCTGGCCTCAATCTACTCCCCGGATCACTCAAGCAA
TAACTTCTGGTCCAGCCCCTCCACCGCCGTGGGCTCCCCCCAGGGCCTGGGAGGGACGTCGCACTAGCCTGGAGCAGGAG
TCCCTGGTGCCTTATCACCCAGCTACGACGGGGGTCTCCACGGCCTGGAGAGTAAGATAGAAGACCACCTGAACGAGGGC
ATCCACGTGCTCTGCAGCTACGCCATGGGCACGGCTAGCAACGTGCACACGCTGCTGCCCGGCCACCGGGCGCTGGCCTT
GGGCTTCGCCGGCCCCATGCTGCTGGTGGGGGCAGCACGCAGGCCTGGTTGGAGGCGAACACCCTGAGGACGGCCCTGCG
GGCAGCGCCAGCTTCATGCACATCCATGTTGCCCTCTCCAGCTAGCCAGGCGCCCTCCCCGACCTCTCTTGGCCTCCCGA
CTCCTGCAGTGGGCTA

Alignment

ORF - retro_ggor_2770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 57.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAYASFGRDAGVGGLTQAGFLSGELALSSPGPLSPSGMKGTSQYYPSYSGSSR-RRAADGSLDTQPKKVR
          G.Y.SFGRDAGV..LTQAGFL.G.LALSSPGPLSPSGMKGTSQYYPSY..SS..R..AD..LDTQP.KV.
Retrocopy GVYSSFGRDAGVRSLTQAGFLPGKLALSSPGPLSPSGMKGTSQYYPSYASSSG<RTEADSGLDTQPTKVG

Parental  KVPPGLPSSVYPPGSGEDYGRDAAAYPSAKTPSSAYPAPFYVADGSLHPSAELWSPPGQAGFGPMLGGGS
          .VPPGLPS..Y.P.SGE.YGRDAAAYPSAKTPSSA.PAPFY.ADGSLHP.AELWS.PGQ.GFGPMLGGGS
Retrocopy NVPPGLPSLAYLPSSGEEYGRDAAAYPSAKTPSSACPAPFYMADGSLHP*AELWSSPGQVGFGPMLGGGS

Parental  SPLPLPPGSGPVGSSGSSSTFGGLHQHERMGYQLHGAEVNGGLPSASSFSSAPGATYGGVSSHTPPVSGA
          SP..LPPGSGPVGS.G.SSTFGGLHQHERMGYQLHGAEVNGGL..AS.FS.APGATYGGVSSHT.PVSGA
Retrocopy SPSSLPPGSGPVGSGGGSSTFGGLHQHERMGYQLHGAEVNGGLLAASTFSLAPGATYGGVSSHT-PVSGA

Parental  DSLLGSRGTTAGSSGDALGKA-LASIYSPDHSSNNFSSSPSTPVGSPQGLAGTSQWPRAGAPGALSPSYD
          D.LLGSRGTTA.SSGDALGKA.LASIYSPDHSSNNF.SSPST.VGSPQGL.GTS..P.AG.PGALSPSYD
Retrocopy DNLLGSRGTTASSSGDALGKA<LASIYSPDHSSNNFWSSPSTAVGSPQGLGGTSH*PGAGVPGALSPSYD

Parental  GGLHGLQSKIEDHLDEAIHVLRSHAVGTAGDMHTLLPGHGALASGFTGPMSL-GGRHAGLVGGSHPEDGL
          GGLHGL.SKIEDHL.E.IHVL.S.A.GTA...HTLLPGH.ALA.GF.GPM.L..G.HAGLVGG.HPEDG.
Retrocopy GGLHGLESKIEDHLNEGIHVLCSYAMGTASNVHTLLPGHRALALGFAGPMLL>WGQHAGLVGGEHPEDGP

Parental  AGSTSLMHNHAALPSQPGTLPDLSRPPDSYSAL
          AGS.S.MH.H.AL.S.PG.LPDLS.PPDS.S.L
Retrocopy AGSASFMHIHVALSS*PGALPDLSWPPDSCSGL

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	8.00 RPM
SRP007412_heart	0.13 RPM	5.16 RPM
SRP007412_kidney	0.00 RPM	6.38 RPM
SRP007412_liver	0.00 RPM	4.19 RPM
SRP007412_testis	0.10 RPM	19.37 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_2770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2770 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4123
Macaca mulatta	retro_mmul_1194

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000071564	1 retrocopy	retro_hsap_4123,
Gorilla gorilla	ENSGGOG00000003667	1 retrocopy	retro_ggor_2770 ,
Macaca mulatta	ENSMMUG00000009017	1 retrocopy	retro_mmul_1194,
Nomascus leucogenys	ENSNLEG00000001742	1 retrocopy	retro_nleu_2472,