RetrogeneDB ID: retro_ggor_2198

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:98871117..98871522(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000006960
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSGGOG00000022928
• Aliases: None
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_ggor_2198
ATGGCTCTTACAAAGCAGACTGCCTGCAAATCCACCGGTGGTGAAGCATCCAGAAAGCAAGTGGCTACAAAAGCCGCCTG
CAAGAGTGCGCCCTCTACTGGAAGGGTGAAGAAGCCTCATTGTTACAGGCCGGTTCTGTGGCACTCCGAGAAATTAAACA
TTATCAGAAGTCCACTGAACTTCCGATTCGCAAACTTCCCTTTCAGCATCTGGTGGAGAAATTGCTCAGGACTTTAAAAC
AGATCTGGGCTCCAGAGCGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGACAC
CAACCTGTGCGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGACATCCAGCTAGCACGTTGCATACGTGGAGAAT
GTGCT

Alignment

ORF - retro_ggor_2198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRP-GTVALREIRRYQKSTELLIRKLPFQ
          MA.TKQTA.KSTGG.A.RKQ.ATKAA.KSAPSTG.VKKPH.YRP.G.VALREI..YQKSTEL.IRKLPFQ
Retrocopy MALTKQTACKSTGGEASRKQVATKAACKSAPSTGRVKKPHCYRP<GSVALREIKHYQKSTELPIRKLPFQ

Parental  RLVR-EIAQDFKTDLR-FQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          .LV..EIAQDFKTDL...QSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR.IRGE.A
Retrocopy HLVE<EIAQDFKTDLG<LQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARCIRGECA

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	161.99 RPM
SRP007412_cerebellum	0.00 RPM	335.67 RPM
SRP007412_heart	0.03 RPM	65.20 RPM
SRP007412_kidney	0.04 RPM	187.19 RPM
SRP007412_liver	0.16 RPM	175.20 RPM
SRP007412_testis	0.10 RPM	607.82 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_2198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2198 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3231
Pan troglodytes	retro_ptro_2183

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Gorilla gorilla	ENSGGOG00000022526	11 retrocopies	retro_ggor_1179, retro_ggor_1809, retro_ggor_1837, retro_ggor_1919, retro_ggor_2003, retro_ggor_2837, retro_ggor_2956, retro_ggor_3082, retro_ggor_393, retro_ggor_736, retro_ggor_944,
Gorilla gorilla	ENSGGOG00000022928	7 retrocopies	retro_ggor_1964, retro_ggor_2181, retro_ggor_2198 , retro_ggor_2357, retro_ggor_2805, retro_ggor_2905, retro_ggor_2987,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,