RetrogeneDB ID: retro_ggor_906

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:120707803..120708339(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000015696
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSGGOG00000011263
• Aliases: None
• Description: None

Sequence

>retro_ggor_906
AACATCTTTGCCAACGTCTTCAAGGGCCTTTTTGACAGAAAAGAAATGTGCATCCTCATGGTGGGCCTGGGTGCTGCAGG
GAAGACCACAGTCCAGTACAAGCTTAAGCTGGGGGAGATGGTGACCACCATTCCCACCATAGGCTTCAACGTGGTAACCA
TGGAGTACAAGAATATTAGCTTCACTGTGTGGGGCGTGGGTGGCTCGGACAAGATCCGACCTCTGTGGTGCCACTACTTC
CAGAACACACAGGCCTGATTTTTGTAGTGGACAGCACTGACAGAGGGCGTATGATTGAGGCCTGTGAGGAGTTCATGAGG
CTGCTGGCCGAGGACGAGCTCTGGGATACTGTCCTCCTGGGGTTTGCCAACAAGCAGGACCTCTCCAACGCCGTGAATGC
AGCAGGGACCACAGACAAGCTGGGGCTGCACTCCCTTTGTCACATGAGCTGGTACATTCAGGCCACCTGTGCCACCAGTG
GCGACGGGCTCTATCAAGGACTGGGCTGGCTGTCTAGTCCGCTCCGGAACCAGAAG

Alignment

ORF - retro_ggor_906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQD
          NIFAN.FKGLF..KEM.ILMVGL.AAGKTT..YKLKLGE.VTTIPTIGFNV.T.EYKNISFTVW.VGG.D
Retrocopy NIFANVFKGLFDRKEMCILMVGLGAAGKTTVQYKLKLGEMVTTIPTIGFNVVTMEYKNISFTVWGVGGSD

Parental  KIRPLWRHYFQNTQ-GLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITD
          KIRPLW.HYFQNTQ.GLIFVVDS.DR.R..EA.EE.MR.LAEDEL.D.VLL.FANKQDL.NA.NAA..TD
Retrocopy KIRPLWCHYFQNTQ<GLIFVVDSTDRGRMIEACEEFMRLLAEDELWDTVLLGFANKQDLSNAVNAAGTTD

Parental  KLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
          KLGLHSL.H..WYIQATCATSGDGLY.GL.WLS..LRNQK
Retrocopy KLGLHSLCHMSWYIQATCATSGDGLYQGLGWLSSPLRNQK

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	217.85 RPM
SRP007412_cerebellum	0.08 RPM	174.61 RPM
SRP007412_heart	0.28 RPM	116.73 RPM
SRP007412_kidney	0.16 RPM	196.80 RPM
SRP007412_liver	0.08 RPM	170.85 RPM
SRP007412_testis	0.00 RPM	303.65 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_906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_906 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1160
Pongo abelii	retro_pabe_965

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000000294	1 retrocopy	retro_ggor_1552,
Gorilla gorilla	ENSGGOG00000004952	1 retrocopy	retro_ggor_373,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906 ,
Gorilla gorilla	ENSGGOG00000016749	1 retrocopy	retro_ggor_1016,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,