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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtaaaaaaaatattctcactcaagcaacaaaacttcttagcttgcacagtggggtcttgctgctgtaaattatgctaatgcgcaccgaacgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT

Basic information

species Zea mays
transcript GRMZM2G155437_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01430.1 (Oryza sativa), 3'ss of exon 1
aagtaaaaaaaatattctcactcaagcaacaaaacttcttagcttgca--cagtggggtcttgctgctgtaaattatgctaatgcgcaccgaacgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT
   |      |   | |  | ||  |||   |    ||||   ||| |   |||  | | |     |   |  |     |  ||| |      ||| |||||| |||||||| ||||||||||||||||| || || ||||||||||||||||| ||  |||| || ||||||||||| ||  | |||   |  ||||||||
-tttttttctatcctgcatattct-gcacagatcgctcttgttttgtaattagttagttatcagcaccaaagctctaatttgtgcccctgattcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAGTTGTTACCGATATCAAAGATGCCGTCGAGCACTACGCTAATGCCTATGT

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 1
aagtaaaaaaaatattctcactcaagcaacaaaacttcttagcttgca--cagtggggtcttgctgctgtaaattatgctaatgcgcaccgaacgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT
   |      |   | |  | ||  |||   |    ||||   ||| |   |||  | | |     |   |  |     |  ||| |      ||| |||||| |||||||| ||||||||||||||||| || || ||||||||||||||||| ||  |||| || ||||||||||| ||  | |||   |  ||||||||
-tttttttctatcctgcatattct-gcacagatcgctcttgttttgtaattagttagttatcagcaccaaatctctaatttgtgcccctgattcgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAGTGGTTACCGATATCAAAGATGCCGTCGAGCACTACGCTAATGCCTATGT
















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|211011964|gb|FL302300.1|FL302300
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211011963|gb|FL302299.1|FL302299
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211520197|gb|FL010166.1|FL010166
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211520200|gb|FL010169.1|FL010169
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|32907095|gb|CF011908.1|CF011908
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211011965|gb|FL302301.1|FL302301
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|15100390|gb|BI396181.1|BI396181
EST:     CCCAAGTCCAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211009195|gb|FL302296.1|FL302296
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211011962|gb|FL302298.1|FL302298
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAG                         TGACCTTATCGAAGGACCAAGAAGAAGCCRGGTTTGGAGCGCAAGGGCAAA
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAA-GACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAA
EST: gi|211520196|gb|FL010165.1|FL010165
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGC-ACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211009194|gb|FL302295.1|FL302295
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211520199|gb|FL010168.1|FL010168
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211520198|gb|FL010167.1|FL010167
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
EST: gi|211011966|gb|FL302302.1|FL302302
EST:     CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGTGCAACCGCCCAG                         TGACTTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG
genomic: CAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 279

CGGCACCGCTAAAACCTAGCAGAGGCTCGTGCCGCCACCGCCAGCCGCAACAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

CGGCACCGCTAAAACCTAGCAGAGGCTCGTGCCGCCACCGCCAGCCGCAACAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

CGGCACCGCTAAAACCTAGCAGAGGCTCGTGCCGCCACCGCCAGCCGCAACAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

CGGCACCGCTAAAACCTAGCAGAGGCTCGTGCCGCCACCGCCAGCCGCAACAAGGAAGGAACCAGGAACACAATGCCCAAGTCCAAGCGCAACCGCCCAGgtgatcccca ... acgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacagtggggtcttgctgctgtaaattatgctaatgcgcaccgaacgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT
                             tgctaat  putative branch site (score: 158)
                      taaattatgctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtaaaaaaaatattctcactcaagcaacaaaacttcttagcttgcacagtggggtcttgctgctgtaaattatgctaatgcgcaccgaacgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTGGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCCGTGGACAAGTACAGCAGCGCCTATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - aaaaaaa
- - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg