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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatatatgatgttatctgttttttcagaacctaaaagttccggtgcccaattaggattcagtttactcaaactcctatgttctaatttcttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA

Basic information

species Zea mays
transcript GRMZM2G047431_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047431_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g16970.2 (Oryza sativa), 3'ss of exon 5
ttaatatatgatgttatc-tgttttttcagaacctaaaagttccggtgcccaattaggattcagtttactcaaactcctatgttctaattt--cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA
   |||| |     |||| |  | ||| |  | |   |||||   |||||   | | |||||| |||| | | ||| || || ||   |||   ||||| ||||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||| ||| |||| |||| ||||||||||||||||||||||||||
---atattttggtctatcatactatttgaagaacctgaagttgtagtgcctcttaatgattcaatttattgagacttctctgctcccctttatttttttccagAAAATATGGTTTGGATGATAATACAATAGACTTTATTGGCCATGCAGTGGCTCTTCATAAAGAGGATAACTACCTGACAGAACCTGCAATTGACACTGTA
















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|5343121|gb|AI795531.1|AI795531
EST:     ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTC                         AAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGC
genomic: ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGC
EST: gi|33771056|gb|CF273350.1|CF273350
EST:     ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTC                         AAAATATGGTTTGGATGATAATACGATAGACTTCATTG
genomic: ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTG
EST: gi|32866625|gb|CF006307.1|CF006307
EST:     ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTC                         AAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGC
genomic: ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGC
EST: gi|148960309|gb|EE153565.2|EE153565
EST:     ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTC                         AAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGC
genomic: ACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGC

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: 45 (upstream exon), 41 (downstream exon)
Score: 55

CTGGGAAATTCTTCCTTTATGTCCAAGATTATAAGGAAAATGACCCAAGTACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 44

CTGGGAAATTCTTCCTTTATGTCCAAGATTATAAGGAAAATGACCCAAGTACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

CTGGGAAATTCTTCCTTTATGTCCAAGATTATAAGGAAAATGACCCAAGTACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 124

CTGGGAAATTCTTCCTTTATGTCCAAGATTATAAGGAAAATGACCCAAGTACTCATAAGGGTTACAACCTTACTAAACTAACGACAAAAGAACTTATCTCgtgggtacct ... cttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcccaattaggattcagtttactcaaactcctatgttctaatttcttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA
                                    ttctaat  putative branch site (score: 124)
                                    ttctaatttctttttt  CT-rich tract
                                    ttctaatttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatatatgatgttatctgttttttcagaacctaaaagttccggtgcccaattaggattcagtttactcaaactcctatgttctaatttcttttttcagAAAATATGGTTTGGATGATAATACGATAGACTTCATTGGGCATGCAGTGGCTCTTCATAGAGATGATAGCTACTTGACAGAACCTGCAATTGACACTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - tgatgtt
- - - - - - - - tctgttt
- - - - - - - - - - - - - cagaacc
- - - - - - - - - - - - - - - - - - - - -ccggtgc