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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattaaggttcctgaattatatgttcttgtacacattatcttatcacattagtaaatttcacactactaaacaaagttccttatgctgtggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC

Basic information

species Zea mays
transcript GRMZM2G023652_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023652_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g36340.1 (Oryza sativa), 3'ss of exon 8
atattaaggttcctgaattatatgttctt--gtacacattatcttatcacattagtaaatttcacactactaaacaaagttccttatgctgtggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC
 | |     | | |    ||| | || |   | ||  |  | ||  || ||||  ||  ||  | |  | |||  |||    || |||      ||| | |||| || ||||||||||||||||| |||||||| ||||||||||||||| ||||||||||  ||||||||||||  ||||||||||||||||||||||| |
gtttccttatacatatgctatcttttgtatggcactaagaacctgttcccattcatat-ttataaagaaataatgaaatcaactcatgtgactattt-gcagATCCCACCAACACGCGCTAGGTCACCAAAGCTTGGCCGGCACAAGCCAACCAATTCTGCTGCTGCTGCTTCTGTTGATGGTTCTGTATCATGTGAGAGTC
















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|32838814|gb|CD978495.1|CD978495
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAG
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAG
EST: gi|22819173|gb|BU499263.1|BU499263
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|60357341|gb|DN224314.1|DN224314
EST:     CAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|22819288|gb|BU499378.1|BU499378
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|21843366|gb|BQ703947.1|BQ703947
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32833164|gb|CD972842.1|CD972842
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAG
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAG
EST: gi|26559955|gb|CA832190.1|CA832190
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAA-                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|87157517|gb|DY402306.1|DY402306
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|21809702|gb|BQ668020.1|BQ668020
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32839274|gb|CD978955.1|CD978955
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGC
EST: gi|7217064|gb|AW563186.1|AW563186
EST:     AAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGNTAGGTCGCCAAAGCTCGGCCGGCCCAAGCCAGCC
genomic: AAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|31355396|gb|CD439753.1|CD439753
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|60356563|gb|DN223536.1|DN223536
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|32837723|gb|CD977401.1|CD977401
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCG
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCG
EST: gi|22542624|gb|BU093062.1|BU093062
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|24769732|gb|CA404861.1|CA404861
EST:     CCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
EST: gi|31355088|gb|CD439445.1|CD439445
EST:     CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAG                         ATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC
genomic: CTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCC

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: 409

AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 462

AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

AGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGTTGAAAAAGgtactgagtt ... ggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacattagtaaatttcacactactaaacaaagttccttatgctgtggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC
                    tactaaa  putative branch site (score: 333)
     tagtaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattaaggttcctgaattatatgttcttgtacacattatcttatcacattagtaaatttcacactactaaacaaagttccttatgctgtggttttgtagATTCCCCCAACACGCGCTAGGTCGCCAAAGCTCGGCCGGCACAAGCCAGCCAATTCTGCCACTGCTGCTTCTGCGGATGGTTCTGTATCATGTGAGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT