RetrogeneDB ID: retro_ggor_1197

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:36331876..36332701(-)
• Located in intron of: ENSGGOG00000008166

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSGGOG00000006130
• Aliases: None
• Description: None

Sequence

>retro_ggor_1197
AAGGGCCATGATTCAAAGGAACCAGAGCTTTTGCAAAAACTTTTTATTGGTGGTCTGAGCTTTAAAACTACAGATGATAG
TTTAAGAGACATTTTGAGAAATGGGGCACACTCACAGATTGTGTGGTAATGAGACCCCAAAAAACACGTTCCAGGGGCTT
TGCTTTTGTGACTTACTCTTGTGTTGAAGAGGTGGAGGCAGCAAGGTGTGCTAGACCACACAAGGCTGATAGGTGTGTAG
TGGGACCAAAGAGAGCTGTTTCTATAGAGGATTCTGTAAAGTCTGGTGCCCATCTAACAGCGAGGAAAATTTTTGTTGGT
GGTATTAAAGAAGAAACAGAAGAATATAATTTGAGAGACTACTTTGAAAAGTATGGCAAGATTGAAACCGCAGAAGTTAT
GGAAGACAGGCAGAGTGGAAAAAAGACAGGATTTGCTTTTATAACTTTTGATGATCATGATACAGTTGATAAAATTGTTG
TTCAGAAATACCACAGTATTAATGGGCATAACTGTGAAGTAAAAAAGGCCCTTTCTAAACAAGAGATGTAGTCTGCTGGA
TGACAGAGGTCATAGAGGTAGATCCGGCAATTTTATTATGGAGGAAACTTTGGAGGTGGTAGAGGTAGTTTTGGCTGTGG
TGGAAACTCTGATGGAAGAGGAGGCTATGGTGGTGAAGGTGGTGGCAGCAGAGGTAGTTATGGACGAGGTGATGGTGGAT
ATAATGGTTTTGGAGGTGATGGTGGCAACTATGGTGGTAGTCCTGGTTACAGTAGTAGAGGGGGCTATGATGGTGATGGA
CCAAGGATATGGTGGTGGTGGTGGA

Alignment

ORF - retro_ggor_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.21 %
• Parental protein coverage: 73.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EGHDPKEPEQLRKLFIGGLSFETTDDSLRE-HFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
          .GHD.KEPE.L.KLFIGGLSF.TTDDSLR..HFEKWGTLTDCVVMR.PQ..RSRGF.FVTYSCVEEV.AA
Retrocopy KGHDSKEPELLQKLFIGGLSFKTTDDSLRD<HFEKWGTLTDCVVMR-PQKTRSRGFAFVTYSCVEEVEAA

Parental  MCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
          .CARPHK.D..VV.PKRAVS.EDSVK.GAHLT..KIFVGGIKE.TEEYNLRDYFEKYGKIET.EVMEDRQ
Retrocopy RCARPHKADRCVVGPKRAVSIEDSVKSGAHLTARKIFVGGIKEETEEYNLRDYFEKYGKIETAEVMEDRQ

Parental  SGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRG-RGGGSGNFMGR-GGNF
          SGKK.GFAF.TFDDHDTVDKIVVQKYH.INGHNCEVKKALSKQEM.SAG.QR..RG..SGNF....G...
Retrocopy SGKKTGFAFITFDDHDTVDKIVVQKYHSINGHNCEVKKALSKQEM*SAG*QRS>RG-RSGNFIME<GNFG

Parental  GGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGP-GYGNQ
          GG.G..FG.GGN..GRGGYGG.GGGSRGSYG.GDGGYNGFGGDGGNYGG.PGYSSRGGY.G.GP.GYG..
Retrocopy GGRG-SFGCGGNSDGRGGYGGEGGGSRGSYGRGDGGYNGFGGDGGNYGGSPGYSSRGGYDGDGP>GYGGG

Parental  GG
          GG
Retrocopy GG

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	162.66 RPM
SRP007412_cerebellum	0.04 RPM	172.01 RPM
SRP007412_heart	0.03 RPM	69.07 RPM
SRP007412_kidney	0.08 RPM	173.21 RPM
SRP007412_liver	0.03 RPM	89.29 RPM
SRP007412_testis	0.10 RPM	377.83 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_1197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1197 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1572
Pan troglodytes	retro_ptro_1059

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000003040	6 retrocopies	retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197 , retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,