RetrogeneDB ID: retro_ggor_1362

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:94212193..94212914(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPIC
• Ensembl ID: ENSGGOG00000024597
• Aliases: None
• Description: None

Sequence

>retro_ggor_1362
ATGACTTGGATTGAACAAGATAAGCTGGGTCAAGCATTTGAAGACGCTTTTGAGGTACTGAGGCGACATCCAACTTTAGA
TCCTCAGAACTCCCCTGATGACAAAAATTACCTGTCTTTCATTAACTGATGTCTTCATATCAGAGGAAATTCCAGCTGCT
ATGAGTGTTGCCTACAGAGGAAGCTGTCTACAATTGGAGAACTGTAATAGCAGGACTGTGGACTTCTATTTTGAAGGAAA
TATTCATCAACCTCTGCAGAGCATAACTGAAAACCAGCTGGTACAACCTGCTCTTCTCCAGCAAGAGGAAGAAAAGGCAG
GAAGAAGCTCTGGCTATTGAATACCTTCACAAATCCCTGTGTAATTCTGAGATGGCATCTTGTATTCACTGGGAAGATAA
AACCAAAGACACCTTTCAGTTTGTAACAAAAAACCAGGAAACTTCTGAACTTTGGGGGAAGAGAAAAAGCAACCAGAGTA
CCATGACTTTCCAGAAATGGCCAGGGCACTGAGGAGCTGTGGAAGAACTGGGGAAATCACCGAAACCCAGTACCATTTCA
GTGAGGCCATTCTCCAAAAACTCTCTCCATCTTACTTCTTGGGGAAAGAGTTCTTCTACTTACAATATGATCAACCTGAT
TAAGAATATATTGGTTTCTATAACTGTGATGCAGATTATAACTATACAAATGCCAATTACCAGAAGCTAAGCCACCCTGA
T

Alignment

ORF - retro_ggor_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 99.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MTCVEQDKLGQAFEDAFEVLRQHSTGDLQYSPDYRNYLALINHRPHVKGNSSCYG-VLPTEEPVYNWRTV
          MT..EQDKLGQAFEDAFEVLR.H.T.D.Q.SPD..NYL..IN...H..GNSSCY..VLPTEE.VYNWRTV
Retrocopy MTWIEQDKLGQAFEDAFEVLRRHPTLDPQNSPDDKNYLSFIN*CLHIRGNSSCYE<VLPTEEAVYNWRTV

Parental  I-NSAADFYLEGNIHQSLQNITENQLVQPTVLQQ-KGGKGRKKLRLF-EYLHESLYNPEMASCIQWVDKT
          I.....DFY.EGNIHQ.LQ.ITENQLVQP..LQQ..G.KGRKKL.L..EYLH.SL.N.EMASCI.W.DKT
Retrocopy I<SRTVDFYFEGNIHQPLQSITENQLVQPALLQQ<RGRKGRKKLWLL<EYLHKSLCNSEMASCIHWEDKT

Parental  KGIFQFVSKNKEKLAELWGKRKGNRKTMTYQK-MARALRNYGRSGEITKIRRKLTYQFSEAILQRLSPSY
          K..FQFV.KN.E...ELWGKRK.N..TMT.QK.MARALR..GR.GEIT.......Y.FSEAILQ.LSPSY
Retrocopy KDTFQFVTKNQET-SELWGKRKSNQSTMTFQK<MARALRSCGRTGEITETQ----YHFSEAILQKLSPSY

Parental  FLGKEIFYSQCVQPDQEYLSLNNWNANYNYTYANYHELNHHD
          FLGKE.FY.Q..QPD.EY....N..A.YNYT.ANY..L.H.D
Retrocopy FLGKEFFYLQYDQPD*EYIGFYNCDADYNYTNANYQKLSHPD

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.13 RPM
SRP007412_testis	0.00 RPM	0.00 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_1362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1362 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3135

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009904	2 retrocopies	retro_btau_1281, retro_btau_1837,
Callithrix jacchus	ENSCJAG00000001906	1 retrocopy	retro_cjac_3835,
Dasypus novemcinctus	ENSDNOG00000004496	1 retrocopy	retro_dnov_759,
Equus caballus	ENSECAG00000009614	1 retrocopy	retro_ecab_542,
Echinops telfairi	ENSETEG00000004217	6 retrocopies	retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Homo sapiens	ENSG00000166211	4 retrocopies	retro_hsap_1748, retro_hsap_1800, retro_hsap_3135, retro_hsap_864,
Gorilla gorilla	ENSGGOG00000024597	4 retrocopies	retro_ggor_1324, retro_ggor_1362 , retro_ggor_2255, retro_ggor_703,
Loxodonta africana	ENSLAFG00000015661	1 retrocopy	retro_lafr_912,
Myotis lucifugus	ENSMLUG00000011052	1 retrocopy	retro_mluc_2169,
Macaca mulatta	ENSMMUG00000020873	1 retrocopy	retro_mmul_1245,
Oryctolagus cuniculus	ENSOCUG00000008070	1 retrocopy	retro_ocun_161,
Otolemur garnettii	ENSOGAG00000015148	1 retrocopy	retro_ogar_1782,
Pongo abelii	ENSPPYG00000004873	4 retrocopies	retro_pabe_1444, retro_pabe_1445, retro_pabe_2819, retro_pabe_686,
Pan troglodytes	ENSPTRG00000005351	4 retrocopies	retro_ptro_1206, retro_ptro_1218, retro_ptro_3070, retro_ptro_598,
Rattus norvegicus	ENSRNOG00000005720	1 retrocopy	retro_rnor_1519,
Ictidomys tridecemlineatus	ENSSTOG00000015457	3 retrocopies	retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus	ENSTTRG00000017205	1 retrocopy	retro_ttru_1708,