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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccctgattcttcttaaccaatctggatgttccttagttcttcgttaccgtcatctgtcacccccatttccttgtcactccattggccccatttctttgtggctaacgctatctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA

Basic information

species Zea mays
transcript GRMZM2G133029_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133029_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g56930.1 (Oryza sativa), 3'ss of exon 9
gtaagccc--ctgattcttcttaaccaatctggatgttccttagttcttcgttaccgtcatctgtcacccccatttccttgtcactccattggccccatttctttgtggctaac--gctatctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA
|||||| |  | || | |||  |     ||      ||| | |  | |||    |  |  |   ||  |  | |     || ||  | | ||  |  | |      || ||      || ||| |||| |||||| | ||||||||||||||||||||| || ||||||||||||||||||||||| || |||||||||||||||||  |  | | |||  |  | |||| 
gtaagctcacccgaattttcagattttgtccatggattcatcacgttttc----cgattcttcttcttcgtcgtcgttgtgacaaacaagtgaaca-actaacgaatgcctgtttttctttcttttggtagGTTCGACGTCGGTGAACGTGACGACGTCGTCGGGGAAGAACCAGTACGTGAACACGGGCCAGTTCGACGTGAACGGAGCGTCGCCGCGGCCGCCGTACAG
















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|14203670|gb|BG837347.1|BG837347
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|32928510|gb|CF033322.1|CF033322
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTA
EST: gi|148961306|gb|EE012031.2|EE012031
EST:     TTTCGTGTATGACTTGGCAAACATGCGCATGGGCGGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: -TTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|32919740|gb|CF024552.1|CF024552
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|88749541|gb|DY533682.1|DY533682
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|84976772|gb|DW475194.1|DW475194
EST:     TTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGGATTACGATT                         GGTCAATGTCGGTGAACGTAACCCACGTCATCAAGGGAAAGAACCCAGTA
genomic: TTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGG-ACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACG-ACGTCATCA-GGGAA-GAACC-AGTA
EST: gi|74234970|gb|DT642884.1|DT642884
EST:     TTCGTGTATGACTTTGGCAA-CATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGA
genomic: TTCGTGTATGACTT-GGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGA
EST: gi|19436560|gb|BM952970.1|BM952970
EST:     ATTCGTGTATGCCTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|148940876|gb|EC885709.2|EC885709
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|32928535|gb|CF033347.1|CF033347
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGT
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGT
EST: gi|19350596|gb|BM895128.1|BM895128
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|32929051|gb|CF033863.1|CF033863
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGT
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGT
EST: gi|74234969|gb|DT642883.1|DT642883
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|113702354|gb|EE679858.1|EE679858
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTAACCACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|32931524|gb|CF036336.1|CF036336
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTAC
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTAC
EST: gi|33100162|gb|CF060122.1|CF060122
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGT
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGT
EST: gi|16916513|gb|BM072876.1|BM072876
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|33095406|gb|CF055400.1|CF055400
EST:     ATTCATATATGACTTGGCAAACATGCGCATGGACTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTA
EST: gi|211451752|gb|FL035074.1|FL035074
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|148983004|gb|EE028899.2|EE028899
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
EST: gi|33099546|gb|CF059506.1|CF059506
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGATTACGATT                         GTTCAATGTCGGTGAACGTGACCACGTCATCAGGGAAGAACCAGT
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGT
EST: gi|148941418|gb|EC886337.2|EC886337
EST:     ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATT                         GTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA
genomic: ATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGA

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 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 52

ATCTTGTTTTAAAGGATAAGATATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 352

ATCTTGTTTTAAAGGATAAGATATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

ATCTTGTTTTAAAGGATAAGATATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

ATCTTGTTTTAAAGGATAAGATATTCGTGTATGACTTGGCAAACATGCGCATGGGCTGGGCGGACTACGATTgtaagcccct ... ctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttgtcactccattggccccatttctttgtggctaacgctatctcttggcagGTTCAATGTCGGTGAACGTGACGACGTCATCAGGGAAGAACCAGTACGTGAACACTGGGCAGTTCGACGTGAACGGCTCCGCACGGCGCGCATCTTACAA
                                 ggctaac  putative branch site (score: 151)
                                         ctatctctt  CT-rich tract
                       atttcttt  TA-rich tract