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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgttgttctcgagatcaagctggctaaatttttttacctttctggtttcattcatcttgtggtagcatttgcagagtgttttcgtcgactgtatctccaaaattcctttcgacgccattcaattgccttcctccgactacattgtgattattgaccaccattgttctctgtactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAAGTATTGCAGAACCAAGCACAAAAGCATCCAGGAAGAAAAATAGAAGGGA

Basic information

species Zea mays
transcript GRMZM2G384298_T02
intron # 5
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|211486342|gb|FK991406.1|FK991406
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489223|gb|FK991421.1|FK991421
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489219|gb|FK991417.1|FK991417
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489216|gb|FK991414.1|FK991414
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489212|gb|FK991410.1|FK991410
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489211|gb|FK991409.1|FK991409
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489213|gb|FK991411.1|FK991411
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211486343|gb|FK991407.1|FK991407
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211492102|gb|FK991430.1|FK991430
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211492097|gb|FK991425.1|FK991425
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489215|gb|FK991413.1|FK991413
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489218|gb|FK991416.1|FK991416
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489217|gb|FK991415.1|FK991415
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489210|gb|FK991408.1|FK991408
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|71774350|gb|DR972228.1|DR972228
EST:     GCCTGTGTGGTAGTGTTGCGGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATG
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATG
EST: gi|211489221|gb|FK991419.1|FK991419
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211492101|gb|FK991429.1|FK991429
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGNCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489214|gb|FK991412.1|FK991412
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211492100|gb|FK991428.1|FK991428
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTTAATATTGCAGTCCAAGGTAAGAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATG-TTTAATATTGCAGTCCAAGGTAAGAA
EST: gi|211492095|gb|FK991423.1|FK991423
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489220|gb|FK991418.1|FK991418
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211492099|gb|FK991427.1|FK991427
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGA-CCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
EST: gi|211489222|gb|FK991420.1|FK991420
EST:     GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAG                         ATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA
genomic: GCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAA

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: 17 (upstream exon), 33 (downstream exon)
Score: 1

ATCATAGTCGAATTGGTGGGCCTGCTAGCGTCCCCAATGGTCGTGTCCTGGCCTGTGTGGTAGTGTTGCCGGACTTCTGATAGTTGCTTCGCCAGTACAGgttggttgtt ... tactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAAGTATTGCAGAACCAAGCACAAAAGCATCCAGGAAGAAAAATAGAAGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcctccgactacattgtgattattgaccaccattgttctctgtactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAAGTATTGCAGAACCAAGCACAAAAGCATCCAGGAAGAAAAATAGAAGGGA
                       tattgac  putative branch site (score: 1)
                                      ttctctgt  putative PPT
                   tgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttgttgttctcgagatcaagctggctaaatttttttacctttctggtttcattcatcttgtggtagcatttgcagagtgttttcgtcgactgtatctccaaaattcctttcgacgccattcaattgccttcctccgactacattgtgattattgaccaccattgttctctgtactacgcagATCATAGTGGAACCATCATGGATGTTTAATATTGCAGTCCAAGGTAAGAAAGTATTGCAGAACCAAGCACAAAAGCATCCAGGAAGAAAAATAGAAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA