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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgatcaatttattggaaaacctgtgtgaagctgtattatggctatttggccaggaacatgttatttctaacattacctactcaccctgcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG

Basic information

species Zea mays
transcript AC207890.3_FGT002
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 15
--------------------------------------------------------------------------------------atgtgatcaatttattggaaaacctgtgtgaagctgtattatg---gctatttggcc--aggaacatgt-----tatttctaacatta-cctactcaccctgcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG
                                                                                      |||    | | | |         |||| |||   || |   ||   || |  | | |  ||  | ||||     | | |       ||   | | ||  |||  | | |||||||||||||| ||||| |||||||||||||||||||| ||||||||||| ||| | ||||||||||| ||||||||||||||||| || ||||||||||
gttcgtgctacttgctacttaacattatgaattgtggtgatcttaaattagttgtcggttagcttctgcatagtctgctgtcacatatgaatgctactcaacattgcttctgtttgagattgaaggctgcttgcaaactagtcacagagatatgtgaaattgtcttcgttgctaatattcccattctgtttatgcagGAAGGGCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGATACTAGGGAGAGAAAGGCTGCTCTCCAGAATCTGGAACAGTTCCAGGAGAAAGCAAAGAAGG
















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|211486829|gb|FL010664.1|FL010664
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211483955|gb|FL010658.1|FL010658
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|33091545|gb|CF051539.1|CF051539
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211486830|gb|FL010665.1|FL010665
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32932574|gb|CF037386.1|CF037386
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32932575|gb|CF037387.1|CF037387
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211483951|gb|FL010654.1|FL010654
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCC-GNCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|31360192|gb|CD444549.1|CD444549
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAG                         GAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG

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: 334

TTCTGGGGGGAAATCAAAAGGACAAGGAACCGGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

TTCTGGGGGGAAATCAAAAGGACAAGGAACCGGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 565

TTCTGGGGGGAAATCAAAAGGACAAGGAACCGGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

TTCTGGGGGGAAATCAAAAGGACAAGGAACCGGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAACGCTACCATGCTTGAGgtttgtgcta ... gcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttggccaggaacatgttatttctaacattacctactcaccctgcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG
                                   tactcac  putative branch site (score: 430)
                  ttatttctaacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgatcaatttattggaaaacctgtgtgaagctgtattatggctatttggccaggaacatgttatttctaacattacctactcaccctgcgtttacagGAAGGGCTTGCCCGGCTCGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGACAAGGCAAAGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - -gaagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacatg