RetrogeneDB ID: retro_ggor_2338

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:47630410..47631531(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSGGOG00000014043
• Aliases: None
• Description: None

Sequence

>retro_ggor_2338
ATGGAAGAAGAGATCCCTGCACTCTTCATTGACAATGGCTCCGGCATGTGAAAAGCGGCTTTGCTGGGACAATGCCCTCC
GAGCCATGTTCCCCTCTGTCATCGGGCACCCCCGGCACCAGGGCGTGATGGTGGGCATGGGCCAGAAGGACTCCTACGTG
GGCGACCAGGCCCAGAGCAAGTGCGGCATCCTGCCCCTGAAGTACCCCATCAAGCATGGCATCGTCACAAACTGGGACGA
CATGGAGAAGATCTGGCACCATGTTTTCTACAACGAGCTGTGCGTGGCTATGGAGGAGCAGGTGGTGCTACTGACCGAGG
CCCCGCTAAATCCCAGGGCCAATAGGGAGAAGATGACTCAGATCATGTTTAAGACCTTCAACACCCAGGCCATGTACATG
GCCATTCAGGCCGTGCTGACCCTCCACAGCTCTGGTTGCACCACTGGCATTGTCATGGACTCTGGAGATGGGGTCACCCA
CACAGTGCTCATCTACGAGGGCCACACCCTCCCTCACACCGTCTTGCATCTGGACCTGGCTGGCCGGGACCTTACTGACT
ACCTCATGAAGATCCCTACCTAGTGCGGCTATAGCTTCAACACCATGGCCAAGTGGAAGATCGTGCGCAACATCAAGGAG
AAGCTATGCTATGTCGCCCTGGACTTCGAGTAGGAGATGGCCACTGCTGTATCCTCTTCCTCCCTGGAGAAGAGCTACGA
GCTGCCTGACAGCCAGGCCATCATTATTAGCAATGAGTGGTTCTCGTGTCCGAGGCAGTGTTCCAGCCTTCCTTCCTGGG
CATGGAATCCTGTGGCATCCATGAAAGTACCTTCAACTCCATCATGAAGTGTGACATGGACATCCCCAAAGACCTGTACG
CCAACACAGTGCTGTCTGGCGTCACCACCTTGTACCCTGGCATCCCCAATAGGATGCAGAAGGAGATCACTGCCCTGGCA
TCCAGCACCATGAAGATCAAGATATCGTGCCCCCAGAGTGCAAGTACTTTGTGTGGATCGGTGGCTCCATCCTGGCCTCA
CTGTCCACCTTCCAGCAGATGTGGATTAGCAAGCAGGAGTACAACGAGTCGGGCCCCTCCATCATCCACCGCAAATGCTT
C

Alignment

ORF - retro_ggor_2338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEEEIAALVIDNGSGMCKA-GFAG-DDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
          MEEEI.AL.IDNGSGM.KA.GFAG.D.A.RA.FPS..G.PRHQGVMVGMGQKDSYVGD.AQSK.GIL.LK
Retrocopy MEEEIPALFIDNGSGM*KA<GFAG<DNALRAMFPSVIGHPRHQGVMVGMGQKDSYVGDQAQSKCGILPLK

Parental  YPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQA
          YPI.HGIVTNWDDMEKIWHH.FYNEL.VA.EE..VLLTEAPLNP.ANREKMTQIMF.TFNT.AMY.AIQA
Retrocopy YPIKHGIVTNWDDMEKIWHHVFYNELCVAMEEQVVLLTEAPLNPRANREKMTQIMFKTFNTQAMYMAIQA

Parental  VLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI
          VL.L..SG.TTGIVMDSGDGVTHTV.IYEG..LPH..L.LDLAGRDLTDYLMKI.T..GYSF.T.A...I
Retrocopy VLTLHSSGCTTGIVMDSGDGVTHTVLIYEGHTLPHTVLHLDLAGRDLTDYLMKIPT*CGYSFNTMAKWKI

Parental  VRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCP-EALFQPSFLGMESCGIHET
          VR.IKEKLCYVALDFE.EMATA.SSSSLEKSYELPD.Q.I.I.NE.F.CP.EA.FQPSFLGMESCGIHE.
Retrocopy VRNIKEKLCYVALDFE*EMATAVSSSSLEKSYELPDSQAIIISNEWFSCP<EAVFQPSFLGMESCGIHES

Parental  TFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKI-IAPPERKYSVWIGGSIL
          TFNSIMKCD.DI.KDLYANTVLSG.TT.YPGI..RMQKEITALA.STMKIKI.I.PPE.KY.VWIGGSIL
Retrocopy TFNSIMKCDMDIPKDLYANTVLSGVTTLYPGIPNRMQKEITALASSTMKIKI<IVPPECKYFVWIGGSIL

Parental  ASLSTFQQMWISKQEYDESGPSIVHRKCF
          ASLSTFQQMWISKQEY.ESGPSI.HRKCF
Retrocopy ASLSTFQQMWISKQEYNESGPSIIHRKCF

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	672.84 RPM
SRP007412_cerebellum	0.00 RPM	420.65 RPM
SRP007412_heart	0.00 RPM	127.52 RPM
SRP007412_kidney	0.00 RPM	875.19 RPM
SRP007412_liver	0.00 RPM	477.05 RPM
SRP007412_testis	0.00 RPM	698.57 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_2338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2338 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3466
Pan troglodytes	retro_ptro_2349
Pongo abelii	retro_pabe_2862

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
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,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sorex araneus	ENSSARG00000012197	1 retrocopy	retro_sara_267,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Tupaia belangeri	ENSTBEG00000010781	1 retrocopy	retro_tbel_422,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,