RetrogeneDB ID: retro_fcat_1903

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:29492772..29493705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX
• Ensembl ID: ENSFCAG00000004779
• Aliases: None
• Description: RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]

Sequence

>retro_fcat_1903
GGAAAAGCCATCAAGGTAGAAGAAGCAACTAAACCATCATTTGAAAGTGGTAGATGTGGACCACCTCCACCTCCAAGAAG
CAGAGGCCCTTCAAGAGGTCTTAGAGGTGGAAGAGGAGGAAGTGGAAGAACCAAGGGACCTCCCTCACGTTGAAGGCACA
TGGATGATGGTGGCTATTCCATGAATTTTAACCTAAGTTCTTCCAGGGGACCACTTCCAGTAAAAAGGATCACCACCACG
AAGTAGCTGTCCTACTCATAAAGATATTCCCCTTTCAGACCAGTTTGCAGCAGCAGTGCAGTGGAAAGAAGAGCTCCTGT
GCAATGTGGAAGAGATAGTTATGAAGGCCCATCTTGAAGTTAACCCCTGCCCTCTTGTAGAGGTGTTTGTTTGTCCCCAA
GGGATGATGGGTATTATACTAAAGGCAGCTATTCAACCAGAGATTATCCAAATTCTTGTGATACAAGGGATTATGCATCA
CCACCAAGAGATTTTACCTACTGTGATTATCATCATTCCAGTTCACATCATAACTACCCATCAAGAGGCTATAGTGATAG
AGATGGCTATGGTCCTGATCTTAACTATTCAGATCTTCCGAGTGGAGCTTCCTATAGAGATTCATATGAAAGTTATGGTA
ACTCACATAGTGCTCCACCTACACGAGGGCCCCTGCCATCTTATGGTGGAAGTAGTCGCTATGATTACAGCAGCTCGCAT
AATGGATATGGTGAAAGTCAAGACAGTTACTCAAGCAGCTGAAGTGATCTCTACTCAAATGATACAGTTGGCAGACAAGA
AAGAGAGCTTTCCCTTTCTATAGAAAGGAGGTATCCCCTTCCATGTGATTCCTACAGCACTTCAAGCTGCAGAGCATCTA
GTAGTGGTAACTTTGGAGGAAGCCAGTCTGATAGAGGGGGAAGAAGAAGCAGA

Alignment

ORF - retro_fcat_1903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.45 %
• Parental protein coverage: 80.56 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNMSSSRG
          GKAIKVE.ATKPSFESGR.GPPPPPRSRGP.RGLRGGRGGSG.T.GPPSR..HMDDGGYSMNFN.SSSRG
Retrocopy GKAIKVEEATKPSFESGRCGPPPPPRSRGPSRGLRGGRGGSGRTKGPPSR*RHMDDGGYSMNFNLSSSRG

Parental  PLPVKR-GPPPRSGGPPPK-RSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRDDG
          PLPVKR..PP.RS..P..K.R..P..PV.SSS....RAPV..GRDSY.GP....PLPS.R.V.LSPRDDG
Retrocopy PLPVKR>SPP-RSSCPTHK<RYSPFRPVCSSSAVERRAPVQCGRDSYEGPS*S*PLPSCRGVCLSPRDDG

Parental  YSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGSYRD
          Y.TK.SYS.RDYP.S.DTRDYA.PPRD.TY.DY.HSSS...YPSRGYSDRDGYG.D..YSD.PSG.SYRD
Retrocopy YYTKGSYSTRDYPNSCDTRDYASPPRDFTYCDYHHSSSHHNYPSRGYSDRDGYGPDLNYSDLPSGASYRD

Parental  SYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPPSM
          SYESYGNS.SAPPTRGP.PSYGGSSRY.DYSSS..GYG.S.DSYSSS.SDLYS...D.VGRQER.L..S.
Retrocopy SYESYGNSHSAPPTRGPLPSYGGSSRY-DYSSSHNGYGESQDSYSSS*SDLYSN--DTVGRQERELSLSI

Parental  ERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSR
          ER.YP.P.DSYS.SS..A...G..GGS.SDRGG.RSR
Retrocopy ERRYPLPCDSYSTSSCRASSSGNFGGSQSDRGGRRSR

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
SRP017611_brain	0.00 RPM	39.94 RPM
SRP017611_kidney	0.00 RPM	44.11 RPM
SRP017611_liver	0.00 RPM	24.56 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1903 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1903 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 49 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,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
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,
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,
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,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,