RetrogeneDB ID: retro_ggor_2983

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:18851950..18852220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLDN
• Ensembl ID: ENSGGOG00000013892
• Aliases: None
• Description: None

Sequence

>retro_ggor_2983
AACAAGGCTGTGGAGCAACTGGCAGAAGGATTGCTTTCTCATTACTTGCCAGATCTGCACAGATCAAAACAAACCCTCCA
GGAACTCACACAGAACCACGTTGTATTGTCAGATACACTGGAACAAGAGATTTCAAAATTTAAAGACTGTCATTCTATGT
TGGATATTAATGCTTTGTTTGCTGAGGCTAAACACTATCCTGCCGAGTTGGTGAATATAAGAAAAGAGATGCTGATGCTT
CATGAAAAAAACATCAAATTTTTTAAAAAA

Alignment

ORF - retro_ggor_2983 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 52.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKAVEQLAEGLLSHYLPDLQRSKQALQELTQNQVVLLDTLEQEISKFKECHSMLDINALVKFAEAKHYHA
          .KAVEQLAEGLLSHYLPDL.RSKQ.LQELTQN.VVL.DTLEQEISKFK.CHSMLDINAL..FAEAKHY.A
Retrocopy NKAVEQLAEGLLSHYLPDLHRSKQTLQELTQNHVVLSDTLEQEISKFKDCHSMLDINAL--FAEAKHYPA

Parental  KLVNIRKEMLMLHEKTSKLKKR
          .LVNIRKEMLMLHEK..K..K.
Retrocopy ELVNIRKEMLMLHEKNIKFFKK

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	0.10 RPM	33.62 RPM
SRP007412_cerebellum	0.00 RPM	19.54 RPM
SRP007412_heart	0.03 RPM	5.07 RPM
SRP007412_kidney	0.08 RPM	31.85 RPM
SRP007412_liver	0.00 RPM	16.93 RPM
SRP007412_testis	0.00 RPM	27.87 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_2983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2983 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012059	7 retrocopies	retro_chof_1342, retro_chof_20, retro_chof_2054, retro_chof_2102, retro_chof_211, retro_chof_248, retro_chof_600,
Dasypus novemcinctus	ENSDNOG00000019785	5 retrocopies	retro_dnov_1687, retro_dnov_1885, retro_dnov_2009, retro_dnov_2411, retro_dnov_275,
Echinops telfairi	ENSETEG00000007378	1 retrocopy	retro_etel_404,
Gorilla gorilla	ENSGGOG00000013892	1 retrocopy	retro_ggor_2983 ,
Macropus eugenii	ENSMEUG00000012636	1 retrocopy	retro_meug_778,
Microcebus murinus	ENSMICG00000005595	1 retrocopy	retro_mmur_1610,
Monodelphis domestica	ENSMODG00000017628	2 retrocopies	retro_mdom_1673, retro_mdom_561,
Oryctolagus cuniculus	ENSOCUG00000017351	1 retrocopy	retro_ocun_1575,
Otolemur garnettii	ENSOGAG00000013706	1 retrocopy	retro_ogar_206,
Pan troglodytes	ENSPTRG00000007038	1 retrocopy	retro_ptro_2949,