RetrogeneDB ID: retro_ggor_2096

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:65014588..65015179(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000014511
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TXNDC9
• Ensembl ID: ENSGGOG00000024615
• Aliases: None
• Description: None

Sequence

>retro_ggor_2096
CCCAGGCTGAACTCTGTACCATTCAGAAGAATGGAAGCTGATGCATCTGTTGACATGTTTTCCAAAGTCCTGGAGAATCA
GCTGCTTCAGACTACCAAACTGGTGGAAGAACATTTGGATTCTGAAATTCAAAAACTGGATCAGATGGATGAGGATGAAT
TGGAACACCTTAAAGAAAAGAGACTCGAGGCACTAAGGAAAGCTCAACAGCAGAAACAAGAATGGCTTTCTAAAGGACAT
GGGGAATACAGAGAAATCCCTAGTGACAGAGACTTTTTTCAAGAAGTCAAGGAGAGTAAAAAAGTGGTTTGCCATTTCTA
CAGAGACTCCACATTCAGGTGTAAAATACCAGACAGATTTCTGGCGATATTGTCCGAGAAACAGCTCGAGACCAAATTTT
TGAAGCTGAATGTGGAAAAAGCACCTTTCCTTTGTGAGAGACTGCATATCAAAGTCATTCCCACACTAGCACTGGTAAAA
GATGGGAAAACACAAGATTATGTTGTTGGGTTTACTGACCTAGGAAATACAGATGACTTCACCACAGAAACTTTAGAATG
GGGGCTCAGTTGTTCTGACATTCTTAATTAC

Alignment

ORF - retro_ggor_2096 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.88 %
• Parental protein coverage: 83.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRLNSVPFGRMEADASVDMFSKVLEHQLLQTTKLVEEHLDSEIQKLDQMDEDELERLKEKRLQALRKAQQ
          PRLNSVPF.RMEADASVDMFSKVLE.QLLQTTKLVEEHLDSEIQKLDQMDEDELE.LKEKRL.ALRKAQQ
Retrocopy PRLNSVPFRRMEADASVDMFSKVLENQLLQTTKLVEEHLDSEIQKLDQMDEDELEHLKEKRLEALRKAQQ

Parental  QKQEWLSKGHGEYREIPSERDFFQEVKESENVVCHFYRDSTFRCKILDRHLAILSKKHLETKFLKLNVEK
          QKQEWLSKGHGEYREIPS.RDFFQEVKES..VVCHFYRDSTFRCKI.DR.LAILS.K.LETKFLKLNVEK
Retrocopy QKQEWLSKGHGEYREIPSDRDFFQEVKESKKVVCHFYRDSTFRCKIPDRFLAILSEKQLETKFLKLNVEK

Parental  APFLCERLRIKVIPTLALLKDGKTQDYVVGFTDLGNTDDFTTETLEWRLGSSDILNY
          APFLCERL.IKVIPTLAL.KDGKTQDYVVGFTDLGNTDDFTTETLEW.L..SDILNY
Retrocopy APFLCERLHIKVIPTLALVKDGKTQDYVVGFTDLGNTDDFTTETLEWGLSCSDILNY

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	4.70 RPM
SRP007412_cerebellum	0.00 RPM	4.22 RPM
SRP007412_heart	0.00 RPM	1.00 RPM
SRP007412_kidney	0.00 RPM	10.51 RPM
SRP007412_liver	0.00 RPM	5.70 RPM
SRP007412_testis	0.00 RPM	8.18 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_2096 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2096 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3042
Pan troglodytes	retro_ptro_1996

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009936	1 retrocopy	retro_cjac_500,
Dipodomys ordii	ENSDORG00000013557	1 retrocopy	retro_dord_141,
Homo sapiens	ENSG00000115514	1 retrocopy	retro_hsap_3042,
Gorilla gorilla	ENSGGOG00000024615	1 retrocopy	retro_ggor_2096 ,
Myotis lucifugus	ENSMLUG00000008110	1 retrocopy	retro_mluc_717,
Mus musculus	ENSMUSG00000058407	2 retrocopies	retro_mmus_2791, retro_mmus_873,
Pan troglodytes	ENSPTRG00000012278	1 retrocopy	retro_ptro_1996,