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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcttactgctaatagtatccagttctgatgcactgaactgaatcctatattatttttctttcccgcaatttttttacatgtatctactattgtttctcttctaaaaatatacttgggattttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC

Basic information

species Zea mays
transcript GRMZM2G099547_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099547_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 6
gtgagttcttactgctaatagtatccagttctgatgcactgaactgaatcctatattatttttctttcccgcaat-ttttttacatgtatctactattgtttctcttctaaaaatatacttgggattttgctcta---agGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGG-AGCAATGTGGTATGCAGTATGCGTC
                                                          |   || || |  |||  | ||||   |  || |  ||||||||| |   ||    |  ||     |  ||    ||   ||||||| |||||||| ||||||||||||||||||||||||||||||||||| || |||||       |   | |   | |   |  | | ||||     || 
---------------------------------------------------------gtgagtcattgctacaaagtattttcttttcatttgttattgtttcacacttattctttgacaaaatacgttatcttatttagGTTGAAGATTTGTCAGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTCCAGCCTTAAATTTGTGGCAGCTCCTAACGGAGCAGAA-GCAGAGGAGGTT
















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|16926773|gb|BM079841.1|BM079841
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|60394679|gb|DN227549.1|DN227549
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|101392937|gb|EB818399.1|EB818399
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATTTAAGCTTTTAATT                         GTTGAGGATTTGTCTCCACGCCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|113859466|gb|DW977016.1|DW977016
EST:     CCTTCAAAGAGGATGGAATAACGAAATCTAAGCTTACTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGT
genomic: CCTTCAAAGAGGATGGAATAAC-AAATCTAAGCTT-CTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGT
EST: gi|211360252|gb|FL253401.1|FL253401
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCGCGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|60348216|gb|DN215189.1|DN215189
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|12045916|gb|BF728146.1|BF728146
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCGAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|148980593|gb|EE027217.2|EE027217
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGGCA-GTGTATG
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGG-CAAGTGTATG
EST: gi|32846204|gb|CD985885.1|CD985885
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCGAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGT
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGT
EST: gi|86471527|gb|DY237897.1|DY237897
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|60337543|gb|DN204516.1|DN204516
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|71433974|gb|DR815024.1|DR815024
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|60351167|gb|DN218140.1|DN218140
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCGAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|32928940|gb|CF033752.1|CF033752
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCGAAGCTTCTAATT                         GGTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGT
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGT
EST: gi|16920282|gb|BM074585.1|BM074585
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|71303362|gb|DR787781.1|DR787781
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|6563795|gb|AW231327.1|AW231327
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|71757029|gb|DR954966.1|DR954966
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|16925502|gb|BM078570.1|BM078570
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|6827273|gb|AW330916.1|AW330916
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCGAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|78117103|gb|DV535490.1|DV535490
EST:     CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
EST: gi|78075508|gb|DV503942.1|DV503942
EST:     CTCAGATGACCCTTCNAAGAGGATGGAATAACAAATCTAAGCTTCTAATT                         GTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA
genomic: CTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTA

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: 159

GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC


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

GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 151

GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 83

GTTCTTGGCCTAAGACTGACTCAGATGACCCTTCAAAGAGGATGGAATAACAAATCTAAGCTTCTAATTgtgagttctt ... ttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtatctactattgtttctcttctaaaaatatacttgggattttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC
                       ttctaaa  putative branch site (score: 83)
                                           ttttgctct  putative PPT
                       ttctaaaaatatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcttactgctaatagtatccagttctgatgcactgaactgaatcctatattatttttctttcccgcaatttttttacatgtatctactattgtttctcttctaaaaatatacttgggattttgctctaagGTTGAGGATTTGTCTGCACGGCAAGTGTATGAGAAGCTCCTAGAAGCTGTACAACCTTAGGCACCCGAGCGATGGAGCAATGTGGTATGCAGTATGCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA