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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactattgtgttcttagctccccacccccctagaatatgtactcccttgaaggtaatattttactgctatcttttgcactggtatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA

Basic information

species Zea mays
transcript GRMZM2G105539_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 8
gtaactattgtgt-tcttagctccccacccccctagaatatgtactcccttgaaggtaatattttactgctatcttttgcactggtatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA
||||  ||| ||| | |    |||||  || |||    |||||| |      |  ||||||     ||  ||| |||     ||| |||||||||||||||||||| ||||| ||| ||||||| ||||||||  |   ||| ||||||||||| || | |||||||||||| |||||| |||| ||||||||  
gtaaagattctgtgtatccattcccccaccaccttctgtatgtatttatc--agtgtaatagccatct-ttatatttccttttggcatttttcagGTGATGGCAATAAGTGAATCAGCAAGACTACATTCTTCCCTAAGAAATGAAAGTGTTCCCGTTAAGAGACTCATTGTTAACCAAATTCTACCACCTTCGT

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 9
----gtaactattgtgttcttagctccccacccccctagaatatgtactcccttga-aggtaatattttactgctatcttttgcactggtatttt-tcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA
    ||| |||   |  ||| |       |  |   |    |   |      |  | | ||| |  || |    |    ||||      || |   ||||||||||||||| ||||||||||| ||| ||  | ||||  || | ||||||| ||||||||| | |||||| ||||| |||||  |||| ||||| || |
taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtatttgttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
















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|87153613|gb|DY398402.1|DY398402
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|5846791|gb|AI999874.1|AI999874
EST:     TTTCCGCGACACGGAATCAACAGAGTTTATANATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTCCGCGACACGGAATCAACAGAGTTTATA-ATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|6973389|gb|AW438083.1|AW438083
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGNGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGNTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|6031284|gb|AW076291.1|AW076291
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|5296253|gb|AI782933.1|AI782933
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|211363054|gb|FL031142.1|FL031142
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|78022914|gb|DV491301.1|DV491301
EST:     ACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: ACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|87152689|gb|DY397478.1|DY397478
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|22489513|gb|BU049436.1|BU049436
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GNGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
EST: gi|33097578|gb|CF057538.1|CF057538
EST:     TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG                         GTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA
genomic: TTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAA

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: 62

GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 41

GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACGgtaactattg ... tatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactcccttgaaggtaatattttactgctatcttttgcactggtatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA
                                             tatttttc  CT-rich tract
            aaggtaatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactattgtgttcttagctccccacccccctagaatatgtactcccttgaaggtaatattttactgctatcttttgcactggtatttttcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA