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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaaccgtcttacacgtcaaatgaaatattatgtcatgaacgattttaacgcagaccagtgtttgtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC

Basic information

species Zea mays
transcript GRMZM2G017086_T04
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 17
gtgagcaaccgtc----ttacacgtcaaatgaaatat--tatg--tcatgaacgattttaacgcagaccagtgtttgtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGG-CGGAGTTGAAGAGTTAGGCCGG--AGTGGTTCTACATTTCTGTGCCGCGAACGCAAC
||||| ||    |     || || | |  |  || ||  ||||  |||||||| | | |||      |   || || |||| ||||| ||||||||||||||||| || ||||| |||||||| ||  |   | || ||| |  |  || | ||    ||     |  | | |      |  | |    
gtgagtaatatacataactaaacattagcttgaacatgttatgattcatgaacaactctaa-----gctgttgcttctctaaacagGCGACTGGCACATGGCTTACATTTGCCTGTACAAAGCTCGTGTTATCTGAATTGGAATGCCAGACAGGCTGATGAGCTGATTTGTTTACATTTCTCAAGT---
















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|211283634|gb|FL461525.1|FL461525
EST:     CAATCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|5871756|gb|AW018227.1|AW018227
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|6342705|gb|AW165529.1|AW165529
EST:     GGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: GGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|13316051|gb|BG410498.1|BG410498
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|4572742|gb|AI586391.1|AI586391
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|33098002|gb|CF057962.1|CF057962
EST:     CAACCCAAACATCCGCAAGGGGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|13316052|gb|BG410499.1|BG410499
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|12968041|gb|BG264988.1|BG264988
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|31363376|gb|CD447733.1|CD447733
EST:     CAATCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|33093667|gb|CF053661.1|CF053661
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|32944644|gb|CF049463.1|CF049463
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|32930721|gb|CF035533.1|CF035533
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|32866634|gb|CF006316.1|CF006316
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|31910881|gb|CD651645.1|CD651645
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATGCAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|67013124|gb|CO441873.1|CO441873
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|32932882|gb|CF037694.1|CF037694
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|13177837|gb|BG349020.1|BG349020
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|16378498|gb|BI992465.1|BI992465
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|12968042|gb|BG264989.1|BG264989
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|50332355|gb|CO527481.1|CO527481
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATTTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|32944893|gb|CF049712.1|CF049712
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACACGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|60352250|gb|DN219223.1|DN219223
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|31558633|gb|CD527845.1|CD527845
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|13177836|gb|BG349019.1|BG349019
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|211211022|gb|FL456134.1|FL456134
EST:     CAATCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAG-CCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
EST: gi|5919412|gb|AW054509.1|AW054509
EST:     CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAG                         GTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT
genomic: CAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGT

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: 822

GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1166

GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 631

GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1070

GAAAATGGATCGAGTTTGATGATGACAACCCAAACATCCGCAAGGAGGAAGACATTTTGAAACTATCTGGTGGAGgtgagcaacc ... gtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaaatattatgtcatgaacgattttaacgcagaccagtgtttgtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC
                        ttttaac  putative branch site (score: 1070)
                                          tttgtct  putative PPT
     aatattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaaccgtcttacacgtcaaatgaaatattatgtcatgaacgattttaacgcagaccagtgtttgtctatacagGTGACTGGCACATGGCTTATATCTGCCTATACAAAGCCCGCATGGCGGAGTTGAAGAGTTAGGCCGGAGTGGTTCTACATTTCTGTGCCGCGAACGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA