RetrogeneDB ID: retro_ggor_657

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:79987844..79988476(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMXL1
• Ensembl ID: ENSGGOG00000006944
• Aliases: None
• Description: None

Sequence

>retro_ggor_657
GCTCCTGTGTCACGTGGAAGAGATAGTTAGTGCGGTCCACCTGGAAGGGAACCGCTGCCCTCTCGTAGAGATGTTTATTT
GCCCCCAAGAGATGATGGGTATTCTACAAAAGACAGTTCTTCAAGCAGAGATTACCCAAGTTCTCGTGATACAAGAGGTT
ATGCACCACCACCACCACGAGATTGTACTTACCGTGATTATGGTCATTTCAGTTCACGTGATGACTATCCATCAAGAGGC
TATAGCGATAGAGATGGATATAATAGTGATCATGACTATTCAGATCATCCAAATGGAGGTTCCTACAGAGATTCATATGA
GAGTTATGGTAACTCAAGTAGTGCTGGACATACACGATGGCCCCTGCCAGCTTACGGTGGAAGCAGTCGCTATGATGATT
ACAGCAGCTCACGTGATGGATATGGTGGAAGTCAGACAGTTACTTAGCCACTGAAGTGATCTCTACTCAAGTGGTCGTGA
TCGGGTTGGCAGACAAGAAAGCGGGCTTCCTCCTTCTATGGAAAGGGGGCACCCTCCTCCACGTGATTCCTACAGCAGTT
CAAGCCACAGAGCACCAAGGTGGTGGCCATGGAGGAAGCCAGTCTGATAGAGGGGGAGGCAGAAGCAGGTAC

Alignment

ORF - retro_ggor_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 54.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APVSRGRDSYGGPPRREPLPSHRDIYLSPRDDVYSTKDSYSSKDYPSSRDTRDYAPPP-RDYTYRDYGHS
          APVSRGRDS..GPP.REPLPS.RD.YL.PRDD.YSTKDS.SS.DYPSSRDTR.YAPPP.RD.TYRDYGH.
Retrocopy APVSRGRDS*CGPPGREPLPSRRDVYLPPRDDGYSTKDSSSSRDYPSSRDTRGYAPPPPRDCTYRDYGHF

Parental  SSRDDYPSRGYSDRDGYGRDRDYSDHPSGGSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDG
          SSRDDYPSRGYSDRDGY..D.DYSDHP.GGSYRDSYESYGNS.SA..TR.P.P.YGGSSRYDDYSSSRDG
Retrocopy SSRDDYPSRGYSDRDGYNSDHDYSDHPNGGSYRDSYESYGNSSSAGHTRWPLPAYGGSSRYDDYSSSRDG

Parental  YGGSR-DSYSSSR-SDLYSSGRDRVGRQERGLPPSMERGYPPPRDSYSSSSHRA-GGG-HGGSQSDRGGG
          YGGS..DSY.....SDLYSSGRDRVGRQE.GLPPSMERG.PPPRDSYSSSSHRA..GG.HGGSQSDRGGG
Retrocopy YGGSQ<DSYLATE<SDLYSSGRDRVGRQESGLPPSMERGHPPPRDSYSSSSHRA>QGGGHGGSQSDRGGG

Parental  RSRY
          RSRY
Retrocopy RSRY

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	0.05 RPM	5.18 RPM
SRP007412_cerebellum	0.16 RPM	3.51 RPM
SRP007412_heart	0.03 RPM	1.97 RPM
SRP007412_kidney	0.00 RPM	6.42 RPM
SRP007412_liver	0.00 RPM	4.41 RPM
SRP007412_testis	0.10 RPM	1.76 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_657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_657 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_800

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657 ,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,