RetrogeneDB ID: retro_ggor_2248

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:40871615..40871915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000157576
• Ensembl ID: ENSGGOG00000013672
• Aliases: None
• Description: None

Sequence

>retro_ggor_2248
ATGCCCAAGAAAAAGGTCAGCTCCACCGAAGGGGCTGCCATGGAAGAGCCCAAGAGGAGATCAGCGCAATTGTCAGCTAA
ACCTCCTGCAAAAGTGGAAGCAAAGCCAAAAAAGGCAGCAGCGAAGGATAAATCTTCAGACACAAAAGTGCAAAAAAAGG
GAAAAGGGGAGCAAAGGGAAAACAGGCCGAAGTGGCTAACCAAAAAACTAAAGAAGATTTACCTGCAGAAAACAGGGGAA
ATGAAAACTGAGGAGAGTCCAGCCTCTGATGAAGCAGGAGATAAAGAAGCCAAGTCTGAT

Alignment

ORF - retro_ggor_2248 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKVSSAEGAAKEEPKRRSARLSAKPPAKVEAKPKKAAAKDKSSDKKVQTKGKRGAKGKQAEVANQET
          MPK.KVSS.EGAA.EEPKRRSA.LSAKPPAKVEAKPKKAAAKDKSSD.......................
Retrocopy MPKKKVSSTEGAAMEEPKRRSAQLSAKPPAKVEAKPKKAAAKDKSSDXXXXXXXXXXXXXXRPKWLTKKL

Parental  KEDLPAENGEMKTEESPASDEAGEKEAKSD
          K.......GEMKTEESPASDEAG.KEAKSD
Retrocopy KKIYLQKTGEMKTEESPASDEAGDKEAKSD

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	0.58 RPM	7.58 RPM
SRP007412_cerebellum	1.06 RPM	10.05 RPM
SRP007412_heart	0.09 RPM	2.81 RPM
SRP007412_kidney	0.53 RPM	17.54 RPM
SRP007412_liver	0.66 RPM	8.49 RPM
SRP007412_testis	0.83 RPM	18.54 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_2248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2248 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1758
Pongo abelii	retro_pabe_1504

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005727	4 retrocopies	retro_cjac_1105, retro_cjac_1412, retro_cjac_2018, retro_cjac_4230,
Gorilla gorilla	ENSGGOG00000013672	6 retrocopies	retro_ggor_107, retro_ggor_145, retro_ggor_16, retro_ggor_2248 , retro_ggor_48, retro_ggor_49,
Otolemur garnettii	ENSOGAG00000033084	3 retrocopies	retro_ogar_1799, retro_ogar_2793, retro_ogar_3104,
Tarsius syrichta	ENSTSYG00000005812	15 retrocopies	retro_tsyr_1029, retro_tsyr_1109, retro_tsyr_1203, retro_tsyr_1209, retro_tsyr_1243, retro_tsyr_1318, retro_tsyr_1904, retro_tsyr_1956, retro_tsyr_310, retro_tsyr_399, retro_tsyr_652, retro_tsyr_664, retro_tsyr_680, retro_tsyr_728, retro_tsyr_913,
Tursiops truncatus	ENSTTRG00000015372	12 retrocopies	retro_ttru_1034, retro_ttru_129, retro_ttru_1511, retro_ttru_1682, retro_ttru_1714, retro_ttru_200, retro_ttru_337, retro_ttru_373, retro_ttru_558, retro_ttru_61, retro_ttru_680, retro_ttru_980,
Vicugna pacos	ENSVPAG00000000013	7 retrocopies	retro_vpac_146, retro_vpac_216, retro_vpac_248, retro_vpac_371, retro_vpac_499, retro_vpac_557, retro_vpac_66,