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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatagcttgaggagagatcttccctacgagatcttcaagctgtttctgtcgtgataggaacagaaagtgtgattaacggcagattccatctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT

Basic information

species Zea mays
transcript GRMZM2G433942_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g70100.1 (Oryza sativa), 3'ss of exon 1
cacatagcttgaggagagatcttccctacgagatcttcaagctgtttctgtcgtgataggaac--agaaagtgtgattaacg---gcagattccatctctt--gcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT
      ||| |||    |||   |  || |||||||||||     |||||      || |||    ||| ||||||||   |     || ||   | ||||   ||||||||| | ||  |||||||||| |||||||| || |||||||||||| |||   ||||||||||||| ||  ||||||| |  ||||| || ||   ||
------gctggagtgatgatag-ctgtatgagatcttcaaatcacttctgcgaatttaagaagtaggaaggtgtgattgcagcttatagcttttgtttctttttcagGTGTTTGTTCTTCAGGGGAGGTTTATATTTGGACCCGATGCAAGATCCTTGTACGTCACCATGTTCCTCATCATCGCGCCAGCGTCAATCTTTTGTTTGT
















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|71330995|gb|DR802320.1|DR802320
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|26558272|gb|CA830507.1|CA830507
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|149046484|gb|EE048006.2|EE048006
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|20512953|gb|BQ280139.1|BQ280139
EST:     GCGCCGGTTGTGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|91868690|gb|EB400117.1|EB400117
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|148953730|gb|EC899096.2|EC899096
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|26456686|gb|CA828269.1|CA828269
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|50332834|gb|CO527960.1|CO527960
EST:     GTGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGGTCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|148990678|gb|EE032074.2|EE032074
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|76921843|gb|DV168729.1|DV168729
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|148944134|gb|EC889222.2|EC889222
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|149106439|gb|EE188329.2|EE188329
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|148973614|gb|EE024722.2|EE024722
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|21987320|gb|BQ778848.1|BQ778848
EST:     GCGCCGG-GGGGAGGCGCCGCTGG-GTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|76017769|gb|DT944939.1|DT944939
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|211006833|gb|FL318418.1|FL318418
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|29167811|gb|CB411071.1|CB411071
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|148943919|gb|EC888999.2|EC888999
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG
EST: gi|211012385|gb|FL318450.1|FL318450
EST:     GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAAT                         GTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTS
genomic: GCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTG

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: 449

ACGGCTATTCGCGGCTGAACGGGCGGCGGCGATGAACGGAGCGAGCGCCGGCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 69

ACGGCTATTCGCGGCTGAACGGGCGGCGGCGATGAACGGAGCGAGCGCCGGCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 23

ACGGCTATTCGCGGCTGAACGGGCGGCGGCGATGAACGGAGCGAGCGCCGGCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

ACGGCTATTCGCGGCTGAACGGGCGGCGGCGATGAACGGAGCGAGCGCCGGCGCCGGCGGGGAGGCGCCGCTGGTGTACAAGGCCTGGAAGGGGAACAATgtgagcggaa ... tctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtcgtgataggaacagaaagtgtgattaacggcagattccatctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT
                           gattaac  putative branch site (score: 302)
                                        ttccatctctt  putative PPT
                          tgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatagcttgaggagagatcttccctacgagatcttcaagctgtttctgtcgtgataggaacagaaagtgtgattaacggcagattccatctcttgcagGTGTTTCTACTGAAGGGGAGGTTCATATTTGGCCCTGATGCAAGATCCCTGTTTATCACCATGTTCCTTATTGTCGCGCCGGTATCAATTTTCTGCGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatt