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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatcactcttgtttctgtcctcaactgacaacagtttgacccacgatagagtatctgttttctgactgtaaacttgtgtattataacag

Basic information

species Zea mays
transcript GRMZM2G017351_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017351_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 8
CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatcactcttgtttctgtcc------------tcaactgacaacagtttgacccacgatagagtat----ctgttttctgactgtaaacttgtgtattataacag
|||||||  |||||||||| ||||||||||||||||| |||||||||||||||||||| || | | ||||||||||||| |||||||||||||| ||| ||| ||||||   | || |||   |              | ||| ||    | ||  | |  |  | || |||     || ||  ||||| |  |||  |||||    ||||
CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttattttatatgacatggattaaccgatggaacttgtagctccagttgaatatatacttgattcttgactatctactattgtatcg--acag
















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|32829924|gb|CD969602.1|CD969602
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|211150022|gb|FL261060.1|FL261060
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATT---ACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|78088124|gb|DV516517.1|DV516517
EST:     AAGGGATTTACGGGAACTCCACCGGAGAGGCAACATAACTCATTGCCACG                         GCCTTCGGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|60397463|gb|DN230279.1|DN230279
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|37397786|gb|CF636201.1|CF636201
EST:     GAGAGGCAACATAACTCGTTACCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: GAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|32830736|gb|CD970414.1|CD970414
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|60341914|gb|DN208887.1|DN208887
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|32831653|gb|CD971331.1|CD971331
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|32831217|gb|CD970895.1|CD970895
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|76284276|gb|DV023844.1|DV023844
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|32831766|gb|CD971444.1|CD971444
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|32831556|gb|CD971234.1|CD971234
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
EST: gi|211097105|gb|FL030452.1|FL030452
EST:     AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCGTTACCACG                         GCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC
genomic: AAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 200

CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAACAGAGGATCTTTCCAAGTGTATAATCAGAGAAAATGCACAGAAGTCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAACAGAGGATCTTTCCAAGTGTATAATCAGAGAAAATGCACAGAAGTCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAACAGAGGATCTTTCCAAGTGTATAATCAGAGAAAATGCACAGAAGTCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 158

CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatc ... attataacagGCCTTCTGTTGTCTATTCAGACAACCAATCACAAAGCACGGCCAATATAACAGAGGATCTTTCCAAGTGTATAATCAGAGAAAATGCACAGAAGTCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTAGATAATTTTAAAAAGCAGTTTGCATACCTTGAGGAACATTATGCCAAGGGATCTACGGGAACTCCACCTGAGAGGCAACATAACTCATTGCCACGgttagatatcactcttgtttctgtcctcaactgacaacagtttgacccacgatagagtatctgttttctgactgtaaacttgtgtattataacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG