RetrogeneDB ID: retro_ggor_2292

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:115024218..115025174(-)
• Located in intron of: ENSGGOG00000016168

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSGGOG00000001133
• Aliases: None
• Description: None

Sequence

>retro_ggor_2292
ACCATGGATAATGATATTGCTGCGCTTGTCGTCGACAATGGCTCTGGCATGTGGAAGGTCTGCTTCACGGGCAACGATGC
CCCTAGGCCGTCTTCCCCTCCATAATGGGGCACCTGAGGCACCAGGGTGTGATGATGGGCATGGGTCAGAAGGACTTCTA
TGTGAGCAACAAGGCCCAGAGCAAGAGAGGTATCATGACCCTGAAGTACCCCATGGAGCATGGCATCGTCACCAACTGGG
ATGACATGGAGAAGATTTGGCACCACACCTTCTACAATGAGCTGCATGTGGCTCCCAAGGAGCACCGTATGCTGCTGACT
GAGGTCCCCCTGAATCCAAGGCCAACCACAAGAAGATGACTCAGATCATGTTTGAGACCTTCAACACCCCAGCCGTGTAT
ATGGCCATCCAGGCCATGCTGTCCCTGTACACCTATGGCCGTACCACTGGCATTGTGATGGACTCCGGCGATGGGGTCAC
CCACACAGTGCTCATCTACGAGGGTTACGTCCTCCCCCGCGCCATCCTGTGTCTGGACGTGGCTGGCCGGGACCTTACTA
ACTACCTCATGAAGATCCTCACCGAGCACAGCTACAGCTTTACCACCATGGCCGAGCGGGAAATCCGTGTGTGACATCAA
GGAGAAGCTATACTATGTCGCCCTGGACTTTGAGCAGGAGATGGCCACAGCGGCCTCCAGCTCCTCCCTGGAGAAGAGCT
ATGAGCTGTCCGATGGCCAGGTCATCACCATTGGCAATGAGCTATCCTGCTGCCCTGAAGCGCTCTTCCAGCCTTCCTTC
CTGAGCATGGAATCCTGTGACATCCACAAAACTATCTTCAGCTCCATCATGAAATGTGACGTGGACATCCGCAAAGACCT
GTACACCAACACAGTGTTGTTTGGCGGCAACAACATGTACCCTGGCATTGCGAACAGGGTGCAGAAGATCATCACT

Alignment

ORF - retro_ggor_2292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TMDDDIAALVVDNGSGMCKAGFAGDDAPR-AVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
          TMD.DIAALVVDNGSGM.K..F.G.DAPR.AVFPSI.G..RHQGVM.GMGQKD.YV...AQSKRGI.TLK
Retrocopy TMDNDIAALVVDNGSGMWKVCFTGNDAPR<AVFPSIMGHLRHQGVMMGMGQKDFYVSNKAQSKRGIMTLK

Parental  YPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNP-KANREKMTQIMFETFNTPAMYVAIQ
          YP.EHGIVTNWDDMEKIWHHTFYNEL.VAP.EH..LLTE.PLNP.KAN..KMTQIMFETFNTPA.Y.AIQ
Retrocopy YPMEHGIVTNWDDMEKIWHHTFYNELHVAPKEHRMLLTEVPLNP<KANHKKMTQIMFETFNTPAVYMAIQ

Parental  AVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAERE
          A.LSLY..GRTTGIVMDSGDGVTHTV.IYEGY.LP.AIL.LD.AGRDLT.YLMKILTE..YSFTT.AERE
Retrocopy AMLSLYTYGRTTGIVMDSGDGVTHTVLIYEGYVLPRAILCLDVAGRDLTNYLMKILTEHSYSFTTMAERE

Parental  I-VRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHE
          I.V.DIKEKL.YVALDFEQEMATAASSSSLEKSYEL.DGQVITIGNE...CPEALFQPSFL.MESC.IH.
Retrocopy I>VCDIKEKLYYVALDFEQEMATAASSSSLEKSYELSDGQVITIGNELSCCPEALFQPSFLSMESCDIHK

Parental  TTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEIT
          T.F.SIMKCDVDIRKDLY.NTVL.GG..MYPGIA.R.QK.IT
Retrocopy TIFSSIMKCDVDIRKDLYTNTVLFGGNNMYPGIANRVQKIIT

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	1553.47 RPM
SRP007412_cerebellum	0.12 RPM	976.01 RPM
SRP007412_heart	0.22 RPM	356.23 RPM
SRP007412_kidney	0.16 RPM	1454.29 RPM
SRP007412_liver	0.24 RPM	1317.16 RPM
SRP007412_testis	0.21 RPM	692.36 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_2292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2292 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3386

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292 , retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,