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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctagctcgtgtatatctttatacttgtagatagaaggttaaatgtcagaaacacgacttcaattgaattctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 3'ss of exon 7
gtaatctagctcgtgtatatctttatacttgtagatagaaggttaaatgtcagaaacacgacttcaattgaattctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG
||||| |    | | | | |  || ||||  | |||     || | |    | || ||     | |    |    | |||||| |||||||| ||||| ||||||||||| || |||||||| || || || || || |||||||| |||||||| ||||||||||| |  |||||||||||
gtaatttcag-catct-tgttcttttactgctggatgt---gtaacaaactaaaatca-----ttagcatatggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTCTTGTAGCAGAGTTCGACTTGGACGAGATCAAGTCTACCAGGCATGGTTG
















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|211141687|gb|FL053515.1|FL053515
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGAC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGAC
EST: gi|78077685|gb|DV506119.1|DV506119
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|211141683|gb|FL053511.1|FL053511
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGTACGAGGAAGTG
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAG-ACGAGGAAGTG
EST: gi|32790714|gb|CD942950.1|CD942950
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|113702021|gb|EE679525.1|EE679525
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|50324198|gb|CO519324.1|CO519324
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|29130437|gb|CB381141.1|CB381141
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|101394654|gb|EB819259.1|EB819259
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         -ACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACAAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGC
EST: gi|32802461|gb|CD954697.1|CD954697
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|84908437|gb|DW404315.1|DW404315
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGAC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGAC
EST: gi|60346678|gb|DN213651.1|DN213651
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|32804827|gb|CD957063.1|CD957063
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|71417126|gb|DR803932.1|DR803932
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCT-CATTGCAG                         GACCAACCGGAAGAA-TAGTG
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGA-GAAATAGTG
EST: gi|29544724|gb|CB605104.1|CB605104
EST:     TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG                         GACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC
genomic: TGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGC

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), 47 (downstream exon)
Score: 236

GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 412

GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 469

GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 344

GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagc ... ttctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtagatagaaggttaaatgtcagaaacacgacttcaattgaattctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG
                                             ttctctgc  CT-rich tract
                                      aattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctagctcgtgtatatctttatacttgtagatagaaggttaaatgtcagaaacacgacttcaattgaattctctgcagGACCAACCGGAGAAATAGTGAAGCTTGCTAACGACAAAGACGAGGAAGTGCTGGTGGCAGAGTTTGACTTGGATGAGATCAAGTCGATTAGGCATGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA