RetrogeneDB ID: retro_ggor_242

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:54032953..54033520(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSGGOG00000001082
• Aliases: None
• Description: None

Sequence

>retro_ggor_242
TTGGCCCTGCTCCCGCGCCCCGCGCTCACCCTCCTGCTCCTCCTCATGGCCGCTGTTATCAGGTGCCTGGAGCAGGCCCA
GACCACCGACCGGATGGCCACCCTGAAGACCATCCGGAACGGCGTTCATAAGATAGACAGGTACCTGAACGCCGCCTTGG
ACCTCCTGGGAGGCGAGGACGGTCTCTGCCAGTATAAATGCAGTGACGGATCTAAGCCTTTCCCACGTTATGGTTATAAA
CCCTTCCCACCGAATGGATGTGGCTCTCCACTGTTTGGCGTTCATCTTAACGTTGGTATCCCTTCCCTGACAAAGTGTTG
CAACCAACACGACAGGTGCTATGAGAACTGTGGCAAAAGCAAGAATGACTGTGATGAGGAATTCCAGTATTGCCTCTCCA
AGATCTGCCGAGAAGTACAGAAAACACTAGGACTAACTTAGCATGTTCAGGCATGTGAAACAACAGTGGAGCTCTTGTTT
GACAGTGTTACACATTTAGGTTGTAAACCATATCTGGACAGCCAACGAGCCGCATGCAGGTGTCATTATGAAGAAAAAAC
CGATCTT

Alignment

ORF - retro_ggor_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLSRPALTLLLLLMAAVVRCQEQAQTTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCSDG
          .ALL.RPALTLLLLLMAAV.RC.EQAQTTD..ATLKTIRNGVHKID.YLNAALDLLGGEDGLCQYKCSDG
Retrocopy LALLPRPALTLLLLLMAAVIRCLEQAQTTDRMATLKTIRNGVHKIDRYLNAALDLLGGEDGLCQYKCSDG

Parental  SKPFPRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRDVQ
          SKPFPRYGYKP.PPNGCGSPLFGVHLN.GIPSLTKCCNQHDRCYE.CGKSKNDCDEEFQYCLSKICR.VQ
Retrocopy SKPFPRYGYKPFPPNGCGSPLFGVHLNVGIPSLTKCCNQHDRCYENCGKSKNDCDEEFQYCLSKICREVQ

Parental  KTLGLTQHVQACETTVELLFDSVIHLGCKPYLDSQRAACRCHYEEKTDL
          KTLGLT.HVQACETTVELLFDSV.HLGCKPYLDSQRAACRCHYEEKTDL
Retrocopy KTLGLT*HVQACETTVELLFDSVTHLGCKPYLDSQRAACRCHYEEKTDL

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	0.19 RPM	7.48 RPM
SRP007412_cerebellum	0.32 RPM	6.89 RPM
SRP007412_heart	0.03 RPM	1.91 RPM
SRP007412_kidney	0.45 RPM	10.67 RPM
SRP007412_liver	0.16 RPM	4.83 RPM
SRP007412_testis	0.41 RPM	10.15 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_242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_242 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_153

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242 , retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,