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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtagtgtggttgcataattcaatgttcttgcttgtgagcccaatttattgttttctctgatgtgtttttctcttcctggttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT

Basic information

species Oryza sativa
transcript LOC_Os10g25090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25090.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 2
gtgggtagtgtggttgcataattcaatgttcttgcttgtgagcccaatttattgtttt-----ctctgatgtgtttttctcttcctggttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT
||| |     ||  | |||| | || |||  || |||   ||     |||  || |||      | |    | | ||| || |  | |  |||  ||||||||||||| |||||| || ||||| |||||||||||||| |||||||||||||| ||  ||||||||||
gtgagctagctg--ttcatagtccactgtagtttcttccaagttttgtttgctgctttgtgccttttctaatatgtttgtcatggttgccctaacagTAAATTGCCGAACTTGGGCCTCTCGGGAAATCTGGCCTACAACATGAACACCATGGATTCATTAGTTGAGCT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88369294|gb|CI577757.1|CI577757
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88311529|gb|CI572585.1|CI572585
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|86888413|gb|CI303695.1|CI303695
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88449338|gb|CI582210.1|CI582210
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88730221|gb|CI753836.1|CI753836
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88385785|gb|CI566647.1|CI566647
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88406193|gb|CI593973.1|CI593973
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|6507597|gb|AU064258.2|AU064258
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88298922|gb|CI567925.1|CI567925
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88720186|gb|CI743485.1|CI743485
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTCCGGGGAATCTGGCCTACAATATGAA-AC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88298740|gb|CI565937.1|CI565937
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGGAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTAAAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88371283|gb|CI600131.1|CI600131
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88314468|gb|CI604952.1|CI604952
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88422824|gb|CI573986.1|CI573986
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88428401|gb|CI564869.1|CI564869
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88392563|gb|CI625385.1|CI625385
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88721915|gb|CI743427.1|CI743427
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88425544|gb|CI569268.1|CI569268
EST:     GCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACA
genomic: GCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGC-AATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACA
EST: gi|88395348|gb|CI611265.1|CI611265
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88385459|gb|CI564119.1|CI564119
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88402885|gb|CI613333.1|CI613333
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88368294|gb|CI577565.1|CI577565
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88300565|gb|CI587369.1|CI587369
EST:     GGCGCCTCATGGCAGGGCATCACCTGGTCTGGATCATCAGTCAAAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88401962|gb|CI593674.1|CI593674
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATTTGGCCTACAATATTAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88405784|gb|CI609683.1|CI609683
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|29631005|gb|CB636014.1|CB636014
EST:     GGCGCCTCATGGCAGGGCTTCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88430712|gb|CI596826.1|CI596826
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88412193|gb|CI573469.1|CI573469
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88415116|gb|CI583939.1|CI583939
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCCTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88396144|gb|CI595692.1|CI595692
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88426869|gb|CI584232.1|CI584232
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTGCAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
EST: gi|88314779|gb|CI608238.1|CI608238
EST:     GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAAT                         TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC
genomic: GGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 69 (downstream exon)
Score: 18

ATTCGCCGGGGCAGCTGCGCGGTTGGCAGGTGAATGGCGGTGACCCATGTGGCGCCTCATGGCAGGGCATCACCTGCTCTGGATCATCAGTCACAGCAATgtgggtagtg ... gttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagcccaatttattgttttctctgatgtgtttttctcttcctggttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT
                     ctctgat  putative branch site (score: 18)
                               tttttctcttcctggt  putative PPT
        aatttattgttttct  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtagtgtggttgcataattcaatgttcttgcttgtgagcccaatttattgttttctctgatgtgtttttctcttcctggttctactagTAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA