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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtatcttttatggtgaaatatttattgccaataattagactgctatctaaatgtcttatggtcatgattgcatgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG

Basic information

species Zea mays
transcript GRMZM2G047894_T02
intron # 15
splice site 3'
intron type U2

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|78021557|gb|DV489944.1|DV489944
EST:     GATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: GATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|71428422|gb|DR809472.1|DR809472
EST:     ATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|32934739|gb|CF039551.1|CF039551
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|5296286|gb|AI783056.1|AI783056
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|31348859|gb|CD433216.1|CD433216
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|40335862|gb|CK369932.1|CK369932
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCNAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCT
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCT
EST: gi|71325384|gb|DR799369.1|DR799369
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|71311517|gb|DR792122.1|DR792122
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|60343346|gb|DN210319.1|DN210319
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|5846902|gb|AI999985.1|AI999985
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
EST: gi|32850672|gb|CD990353.1|CD990353
EST:     ATCTGAAAGCATTTCTCTCTCTGATAACATTCGTGATACATTCAAAAAAT                         TATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG
genomic: ATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATG

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: 49 (upstream exon), 49 (downstream exon)
Score: 130

GCAAGAAAATCATTGGATTCTCAATTGCAGCTGATGGGAGCATTATTGTCATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GCAAGAAAATCATTGGATTCTCAATTGCAGCTGATGGGAGCATTATTGTCATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GCAAGAAAATCATTGGATTCTCAATTGCAGCTGATGGGAGCATTATTGTCATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GCAAGAAAATCATTGGATTCTCAATTGCAGCTGATGGGAGCATTATTGTCATCTGAAAGCATTTCTCTCTCTGATAACATTCATGATACATTCAAAAAATgtaaggtatc ... tgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaataattagactgctatctaaatgtcttatggtcatgattgcatgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG
                 atctaaa  putative branch site (score: 176)
                tatctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtatcttttatggtgaaatatttattgccaataattagactgctatctaaatgtcttatggtcatgattgcatgcctagcagTATGGGTTGAGCACGGTGATGAGCTGAGCCTGGAGTATGCTGGCTCTTATGCTTTGAAAGGGGATCTAGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG