RetrogeneDB ID: retro_ggor_1946

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:71127017..71127681(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H1FOO
• Ensembl ID: ENSGGOG00000000735
• Aliases: None
• Description: None

Sequence

>retro_ggor_1946
GTGGTAGAGGCGCTGCAGGCTGGGGAGTAGCGCTAGGGCACGTTGGCGGTGGCCGTCAAGCTCTACATCCTGCACAAGTA
CCCAACGGTGGACGTCCTCCGCTTAAGGTACCTGCTGAAGCAGGCGCTGGCCACTGGCATGTGCCGCAGCCTCCTCGCCA
GGCCCCTCAACTCCGAAGCCAGGGGGGCCACTGGCAGCTTCAAATTAGATCCCAAGCACAAGAGGAAAATCCAGCCCAGG
GAGATGGCCCCCTGATGGTCCCCAGGAGAGCGGAAAAGGCCAGGGGGAAGTACCCCAAGAAACCAAGTGAGGCCACGGAG
GATCCTCCTAACGCGGGCAAGGTGAAGAAGGCAGCGAAGAGGCCAGCAGAGGTGCAGAAGGCTCCTCTCAAGCCAGGTGC
AGCCGCAGAGAAGGCCGGCAAGCAAGGCAGTGTGGCCAAGGACACCAGGCCACAGCCCGGTGAGGCTAGGAAGGCACCCC
TAAGCCAGACAAGGCCACGCAGGTCCCTTCCAGTGCCAGCGGGCTTAGTAGGAAGGCAAAGGCCAGAGGCAGCAGGAGCA
GCCGGGGAGATGCTGGGGACCACAGGAAAATGAAAGCTGGGAGTAAGACTTCAAAACCCACTGTCAGCAAGGTCAAGAAT
GGTGTTGCTTCCTCGACCAGAAGG

Alignment

ORF - retro_ggor_1946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLEALQAGEQRRGTSVAAIKLYILHKYPTVDVLRFKYLLKQALATGMRRGLLTRPLNSKARGATGSFKLV
          V.EALQAGE.R.GT...A.KLYILHKYPTVDVLR..YLLKQALATGM.R.LL.RPLNS.ARGATGSFKL.
Retrocopy VVEALQAGE*R*GTLAVAVKLYILHKYPTVDVLRLRYLLKQALATGMCRSLLARPLNSEARGATGSFKLD

Parental  PKHKKKIQPRKMV-PATAPRRAGEAKGKGLKKPSEAKEDPPNVGKVKKAAKRPAKVQKAPPKPGAATEKA
          PKHK.KIQPR.M..P...PRRA..A.GK..KKPSEA.EDPPN.GKVKKAAKRPA.VQKAP.KPGAA.EKA
Retrocopy PKHKRKIQPREMA<PLMVPRRAEKARGKYPKKPSEATEDPPNAGKVKKAAKRPAEVQKAPLKPGAAAEKA

Parental  RKQGGVAKDTRAQSGEARKVP-PKPDKAMRAPSSAGGLSRKAKAKGSRSSQGDAEAYRKTKAESKSSKPT
          .KQG.VAKDTR.Q.GEARK.P.PKPDKA...PSSA.GLSRKAKA.GSRSS.GDA...RK.KA.SK.SKPT
Retrocopy GKQGSVAKDTRPQPGEARKAP<PKPDKATQVPSSASGLSRKAKARGSRSSRGDAGDHRKMKAGSKTSKPT

Parental  ASKVKNGAASPTKK
          .SKVKNG.AS.T..
Retrocopy VSKVKNGVASSTRR

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	0.05 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.09 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	4.97 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_1946 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1946 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2799
Pan troglodytes	retro_ptro_1896
Pongo abelii	retro_pabe_2225

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976, retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139, retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946 ,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403, retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111,