RetrogeneDB ID: retro_ggor_2890

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:23482570..23482928(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSGGOG00000007908
• Aliases: None
• Description: None

Sequence

>retro_ggor_2890
ATGCAGGATCCCAATGAAGATACAGAATGGAATGACATTTTAAGAGATTTCGGCATTCTTCCTCCTAAAGAAGAGTCAAA
AGATGAAATTGAAGAAATGGTTTTACGTTTACAGAAAGAAGCAATGGTGAAACCATTTGAAAAGATGACTCTTGCACAGC
TAAAGGAAGCTGAAGATGAATTTGATGAAGAAGATATGCAAGCTATTGAAACATAGAAAGAAGCGGTTACAGGAATGGAA
AGCTCTTAAGAAAAAACAAAAATTTGGAGAATTAACAGAAATTTCTGGAAATCAGTAAGTGAATGAAGTCACAAATGCAG
AAAAAGATGTGTGGGTTATAATTCATCTATACAGATCA

Alignment

ORF - retro_ggor_2890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 63.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQDPNEDTEWNDILRDFGILPPKEESKDEIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQAIE
          MQDPNEDTEWNDILRDFGILPPKEESKDEIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQAIE
Retrocopy MQDPNEDTEWNDILRDFGILPPKEESKDEIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQAIE

Parental  T-YRKKRLQEWKALKK-KQKFGELREISGNQYVNEVTNAEEDVWVIIHLYRS
          T..........K.L.K.KQKFGEL.EISGNQ.VNEVTNAE.DVWVIIHLYRS
Retrocopy T<IERSGYRNGKLLRK<KQKFGELTEISGNQ*VNEVTNAEKDVWVIIHLYRS

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	18.96 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_2890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2890 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890 ,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784, retro_ptro_675,