RetrogeneDB ID:

retro_btau_776

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:19:1923401..1924249(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RNPS1
Ensembl ID:ENSBTAG00000009969
Aliases:None
Description:RNA-binding protein with serine-rich domain 1 [Source:UniProtKB/Swiss-Prot;Acc:A6QR16]


Retrocopy-Parental alignment summary:






>retro_btau_776
ATGGATTTATCAGAAGTGAAAGAGAAGAGCTTGGTAAGAGTTAAAGAAAACAATTTTGAGAAGTCCAGTGCTCGAGCACT
TTCTCTGATCAAATGCGAAGAACGCTCTGATGAGATGTCCAAGGATCACTCTAAAGATAGAGTGTACACCAAGGGGTAGA
GGAAGAAAGACTGTGGCAGGAGTAAGACTCGGGAGAGGTGCAGTGGTTCCAGTGGGAGCAGTAGCACCAGGTCTCAGTGC
AACTCTACTTTCAGTTCGGTCTCCAGCCCAGCACTGGCTCCAGTTTGTCTTCAGCTTGGAGCCACTTAGGGAGTTCCAGC
ACATTCTGCAGCTCCAGCTTCAGCAGCTTCTCTGCCTCTCCATGTACATTACTGCACAGACATGAGAACAGGCGGCATTG
CAGCTCCAAGTCCAAATCATTCAAAAGAGATGAAAAAGAAAGGAAAAAGCAGAGTCTTTCCCAAAACCCACCAAAGTACA
CATTAGGAGGCTCACCAGGAATGTGTCCAGGACCACATCATGGAGATATTCTCCACCTATGGGAAAATTAAAATGATTGA
CATTCCTGTGGAAAGGATGCACCCTCATCTCTCTAAAGATTACACACATGTGGAATTTGAGAATCCAGATGAGGCTGAGA
AGGCTGTGAAACACATGGACAGAGCACAAATAGATGGCCAGGAGATCACTGCTGCCACTGTGCTGGCCCTCTGGCCTTGG
CCACCCCCAGGTGATTCAGCCCTCCCGAGAGCATACCATCTCCCATGCACTGAAGGTCACTCCCACGGATGTGGAGAAGG
TCGCGTTCCCCTTGCTGCAGGTCCTCTGTGAGGCACACTCCCTCTTCC

ORF - retro_btau_776 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.95 %
Parental protein coverage: 94.75 %
Number of stop codons detected: 3
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMDLSGVKKKSLLGVKENN-KKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSAS
MDLS.VK.KSL..VKENN..KSS.RA.S..K...RSDE.SKD.SKD...TK....KD.GR.KTR.R....
RetrocopyMDLSEVKEKSLVRVKENNFEKSSARALSLIKCEERSDEMSKDHSKDRVYTKG*RKKDCGRSKTRER---C
ParentalSGSSSTRSRSSSTSSSGSSTSTGS-SSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSR
SGSS...S...S...S..S......S.GSS.SSA.S..GSSST..SSS.SS.S.SP.....RH.NRR...
RetrocopySGSSGS-SSTRSQCNSTFSSVSSP<STGSSLSSAWSHLGSSSTFCSSSFSSFSASPCTLLHRHENRRHCS
ParentalSKSKPPKRDEKERKRRSPS-PKPTKVHIGRLTRNVTK-DHIMEIFSTYGKIKMIDMPVERMHPHLSKGYA
SKSK..KRDEKERK..S.S.PKPTKVHI.RLTRNV...DHIMEIFSTYGKIKMID.PVERMHPHLSK.Y.
RetrocopySKSKSFKRDEKERKKQSLS<PKPTKVHIRRLTRNVSR<DHIMEIFSTYGKIKMIDIPVERMHPHLSKDYT
ParentalYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPP-PRRFSPPRRMLPPLPMWRRSPPRMRRRSR
.VEFENPDEAEKA.KHMD..QIDGQEITA..VLA.WP.PP.PR.FSPP.....P.PM..RS.PRM.RRSR
RetrocopyHVEFENPDEAEKAVKHMDRAQIDGQEITAATVLALWPWPP<PR*FSPPESI--PSPMH*RSLPRMWRRSR
ParentalSPRRRSPARRRSRS
SP..RS..R....S
RetrocopySPCCRSSVRHTPSS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .00 RPM 38 .07 RPM
ERP005899_muscle 0 .00 RPM 64 .03 RPM
SRP017611_brain 0 .00 RPM 71 .76 RPM
SRP017611_kidney 0 .00 RPM 66 .62 RPM
SRP017611_liver 0 .00 RPM 43 .49 RPM
SRP030211_testis 0 .00 RPM 81 .86 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_776 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_776 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_776 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG00000009969 7 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776 , retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,


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