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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtctgctaggtgtgcctcgggaagctaggattgaacctttcttgcacacttgcatcatagaattgtaatctcacttgtatcttttattctcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG

Basic information

species Zea mays
transcript GRMZM2G134389_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134389_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g10650.1 (Oryza sativa), 3'ss of exon 3
ggtctgctaggtgtgcctcgggaagctaggattgaacctttcttgcacacttgcatcatagaattgta-atctcacttgtatcttttattctcctt--tgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
            || |  |    | |||  | |   |     | |||| ||||||||| |  |||  | | |||  |     || ||  | | |||  | |||||  || ||||||||||||||||||||| || ||||||||||||
------------gtactgcaattatcta--actctcctcacatcgcacgcttgcatcacaacatttcagacctctttaactcctgttgcttttcttgatacagACGTAAAAAACCAACCTCTGCTTATTCACTGCAAGAGAGGCAAG
















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|211509867|gb|FL433772.1|FL433772
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|5555286|gb|AI881237.1|AI881237
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGCCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|5555280|gb|AI881231.1|AI881231
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|5555378|gb|AI881329.1|AI881329
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|93281321|gb|EB673585.1|EB673585
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|50339825|gb|CO534951.1|CO534951
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|32845463|gb|CD985144.1|CD985144
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
EST: gi|78087468|gb|DV515861.1|DV515861
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTA
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTA
EST: gi|76294316|gb|DV033884.1|DV033884
EST:     TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCCAGAAACCAACCTCTGCTTA
genomic: TGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTA

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), 44 (downstream exon)
Score: 67

GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 186

GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 88

GAACCATTTGTCAATATACCCGATGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacttgcatcatagaattgtaatctcacttgtatcttttattctcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG
                       atctcac  putative branch site (score: 88)
                        tctcacttgtatcttt  CT-rich tract
                              ttgtatcttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtctgctaggtgtgcctcgggaagctaggattgaacctttcttgcacacttgcatcatagaattgtaatctcacttgtatcttttattctcctttgcagACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- -ctgctag
- - - - - - -tgcctcg
- - - - - - - - - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - acttgca