RetrogeneDB ID: retro_btau_540

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:30793170..30793655(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOA
• Ensembl ID: ENSBTAG00000004279
• Aliases: RHOA, ARHA
• Description: Transforming protein RhoA [Source:UniProtKB/Swiss-Prot;Acc:P61585]

Sequence

>retro_btau_540
GTGGCCACCATCCAGAAGGAACTGGTGATTGTTGGAGATGGAGCCTGTGACAAGACTTGCTTGATCACTGCCCTTAGCAA
AGACTAATTCCCAGAGGTGTATGTACCCACGGTGTCTGAAAACCATGTGGCAGATGTTGAAGGGGACGGAGAGCAGGTAG
AGTTGGCTTTGTGGGACACAGGTGGGCATGAAGCTTAAGATCACTTGAGGCCTCTCTCCTACCAGGATGCTGATGTAATG
TTGATGTGTTTCTCCACTGACAACTCTGATAGTTTAGAAAACATCCGGAAAAGTGAACTCCGGAAGTCAAGCATTTCCAT
CCCAACATGAGCATCATCCTGGTTGGGAACAAAAAGGATCTTTGAAACTGAGCACACAAGTCAGAAGTAACCAAGAGGAA
ATAGGAGCCAGTAAAACTGGAAGACAGCAAAGATGTGGCAAACACGACTGGTGAAAAAGGAGAGTTGAGAGATGAAGCTA
GAAGT

Alignment

ORF - retro_btau_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.24 %
• Parental protein coverage: 84.46 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
          .A.I.K.LVIVGDGAC.KTCL....SKD.FPEVYVPTV.EN.VAD.E.DG.QVELALWDT.G.E..D.LR
Retrocopy VATIQKELVIVGDGACDKTCLITALSKD*FPEVYVPTVSENHVADVEGDGEQVELALWDTGGHEA*DHLR

Parental  PLSYPDTDVILMCFSIDSPDSLENI-PEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPV
          PLSY.D.DV.LMCFS.D..DSLENI.PEK.TPEVKHF.PN..IILVGNKKDL.N..H...E..K.K.EPV
Retrocopy PLSYQDADVMLMCFSTDNSDSLENI<PEK*TPEVKHFHPNMSIILVGNKKDL*N*AH-KSEVTKRK*EPV

Parental  KPEEGRDMANRIGAFGYMECSAKT
          K.E...D.AN..G..G.....A..
Retrocopy KLEDSKDVANTTGEKGELRDEARS

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
ERP005899_liver	0.00 RPM	50.61 RPM
ERP005899_muscle	0.00 RPM	199.49 RPM
SRP017611_brain	0.00 RPM	83.18 RPM
SRP017611_kidney	0.00 RPM	185.16 RPM
SRP017611_liver	0.00 RPM	60.41 RPM
SRP030211_testis	0.00 RPM	140.81 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_540 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_540 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 37 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008297	1 retrocopy	retro_acar_41,
Ailuropoda melanoleuca	ENSAMEG00000012584	3 retrocopies	retro_amel_101, retro_amel_1515, retro_amel_615,
Anas platyrhynchos	ENSAPLG00000014687	1 retrocopy	retro_apla_10,
Bos taurus	ENSBTAG00000004279	2 retrocopies	retro_btau_206, retro_btau_540 ,
Bos taurus	ENSBTAG00000014299	1 retrocopy	retro_btau_1171,
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Dasypus novemcinctus	ENSDNOG00000012825	6 retrocopies	retro_dnov_1012, retro_dnov_1814, retro_dnov_1904, retro_dnov_2090, retro_dnov_29, retro_dnov_326,
Dipodomys ordii	ENSDORG00000003382	3 retrocopies	retro_dord_1, retro_dord_18, retro_dord_538,
Felis catus	ENSFCAG00000027456	1 retrocopy	retro_fcat_29,
Gasterosteus aculeatus	ENSGACG00000005670	1 retrocopy	retro_gacu_9,
Gallus gallus	ENSGALG00000003806	1 retrocopy	retro_ggal_5,
Gorilla gorilla	ENSGGOG00000012843	1 retrocopy	retro_ggor_2450,
Gadus morhua	ENSGMOG00000008188	1 retrocopy	retro_gmor_18,
Latimeria chalumnae	ENSLACG00000016941	1 retrocopy	retro_lcha_15,
Loxodonta africana	ENSLAFG00000009726	8 retrocopies	retro_lafr_1196, retro_lafr_1197, retro_lafr_1198, retro_lafr_178, retro_lafr_203, retro_lafr_261, retro_lafr_392, retro_lafr_82,
Meleagris gallopavo	ENSMGAG00000002280	1 retrocopy	retro_mgal_2,
Myotis lucifugus	ENSMLUG00000013911	6 retrocopies	retro_mluc_108, retro_mluc_193, retro_mluc_1976, retro_mluc_2553, retro_mluc_2554, retro_mluc_2555,
Macaca mulatta	ENSMMUG00000012962	1 retrocopy	retro_mmul_977,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Mus musculus	ENSMUSG00000007815	9 retrocopies	retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Nomascus leucogenys	ENSNLEG00000006839	4 retrocopies	retro_nleu_104, retro_nleu_2207, retro_nleu_377, retro_nleu_814,
Ornithorhynchus anatinus	ENSOANG00000013807	1 retrocopy	retro_oana_7,
Oryctolagus cuniculus	ENSOCUG00000013323	3 retrocopies	retro_ocun_1075, retro_ocun_726, retro_ocun_854,
Otolemur garnettii	ENSOGAG00000028489	1 retrocopy	retro_ogar_2340,
Oreochromis niloticus	ENSONIG00000018884	1 retrocopy	retro_onil_32,
Procavia capensis	ENSPCAG00000009699	3 retrocopies	retro_pcap_191, retro_pcap_202, retro_pcap_98,
Pelodiscus sinensis	ENSPSIG00000015328	1 retrocopy	retro_psin_7,
Pan troglodytes	ENSPTRG00000014922	3 retrocopies	retro_ptro_10, retro_ptro_2456, retro_ptro_625,
Pteropus vampyrus	ENSPVAG00000008738	1 retrocopy	retro_pvam_599,
Rattus norvegicus	ENSRNOG00000050519	3 retrocopies	retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Sarcophilus harrisii	ENSSHAG00000016308	2 retrocopies	retro_shar_60, retro_shar_96,
Sus scrofa	ENSSSCG00000022080	1 retrocopy	retro_sscr_72,
Ictidomys tridecemlineatus	ENSSTOG00000004561	2 retrocopies	retro_itri_39, retro_itri_96,
Takifugu rubripes	ENSTRUG00000011944	1 retrocopy	retro_trub_19,
Tarsius syrichta	ENSTSYG00000008220	3 retrocopies	retro_tsyr_1604, retro_tsyr_413, retro_tsyr_593,
Vicugna pacos	ENSVPAG00000010931	3 retrocopies	retro_vpac_130, retro_vpac_24, retro_vpac_492,