RetrogeneDB ID: retro_ggor_1040

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:30484617..30485170(+)
• Located in intron of: ENSGGOG00000024205

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK16
• Ensembl ID: ENSGGOG00000010907
• Aliases: None
• Description: None

Sequence

>retro_ggor_1040
CTGGGGGAGAGTGGGTTCAGCCATGTGGACCTAGTGGAGGGGTTACAGGATGGACACTTCTACGCCCTGAAGCGAATCCT
GTGTCACGAGCAGCAGGACTGGGAGGAGGCCCAGCCAAGAAGCGAACATGCATCACCTCTTCAATCACCCCAACATCCTT
TACCTCACGGCTTACTGTCTGAGGGAGTAGGGTGCTAAGCATGAGGCCCAGCTGCTGCTTCCGTTCTTTAAGAGAGATAT
ACTGTGGAATGGAGAGAAAGGCCGAAGGACGATGGCAACTTCCTGACTTAGGATCAAATCCTTCAGCTCCTGCTGGGTAT
CTACAGCGGCTTGAGGCCATTCATGCCAAGGGTTAGGCCCACAGGGACCTGAAGCCCACCACTATCTTGCTTGGAGATGA
GGGGCAGCCAGTTTTAATACACTTGGATGCCATGAATCAAGCATGCCTCACATGAAGGGCTCCCACCAGGCCCTGACCCT
GCCGGACTAGGCGACCCAGCAGTGCACCATCTCCTACTGAGCCCTAGAGCTCTTCCCTGAGCAGTCACTGTGT

Alignment

ORF - retro_ggor_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LAHSGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQ-READMHRLFNHPNILRLVAYCLRERGAKHEA
          L..SGFS.VDLVEGL.DGHFYALKRILCHEQQD.EEAQ..EA.MH.LFNHPNIL.L.AYCLRE.GAKHEA
Retrocopy LGESGFSHVDLVEGLQDGHFYALKRILCHEQQDWEEAQ>QEANMHHLFNHPNILYLTAYCLRE*GAKHEA

Parental  WLLLPFFKRGTLWNE-IERLKDKGNFLTEDQILWLLLGICRG-LEAIHAKGYAHRDLKPTNILLGDEGQP
          .LLLPFFKR..LWN...ER.KD.GNFLT.DQIL.LLLGI..G.LEAIHAKG.AHRDLKPT.ILLGDEGQP
Retrocopy QLLLPFFKRDILWNG<RERPKDDGNFLT*DQILQLLLGIYSG<LEAIHAKG*AHRDLKPTTILLGDEGQP

Parental  VLMDLGSMNQACI-HVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHC
          VL..L..MNQAC..H..GS.QALTL.D.A.Q.CTISY.A.ELF..QS.C
Retrocopy VLIHLDAMNQACL<HMKGSHQALTLPD*ATQQCTISY*ALELFPEQSLC

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	17.55 RPM
SRP007412_cerebellum	0.04 RPM	9.06 RPM
SRP007412_heart	0.00 RPM	8.04 RPM
SRP007412_kidney	0.00 RPM	28.79 RPM
SRP007412_liver	0.00 RPM	23.61 RPM
SRP007412_testis	0.00 RPM	26.83 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_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1040 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1334
Pan troglodytes	retro_ptro_911
Pongo abelii	retro_pabe_1108

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000152	1 retrocopy	retro_dord_692,
Equus caballus	ENSECAG00000014093	1 retrocopy	retro_ecab_166,
Homo sapiens	ENSG00000115661	1 retrocopy	retro_hsap_1334,
Gorilla gorilla	ENSGGOG00000010907	1 retrocopy	retro_ggor_1040 ,
Macropus eugenii	ENSMEUG00000006422	1 retrocopy	retro_meug_1579,
Myotis lucifugus	ENSMLUG00000008066	1 retrocopy	retro_mluc_1213,
Pongo abelii	ENSPPYG00000013202	1 retrocopy	retro_pabe_1108,
Pan troglodytes	ENSPTRG00000012948	1 retrocopy	retro_ptro_911,
Ictidomys tridecemlineatus	ENSSTOG00000025197	2 retrocopies	retro_itri_1662, retro_itri_602,