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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtatgggagtagctcttctcattctccatgctttagctaccaatcttgtagattctgagatataatgaacattgttcttgtttctttgattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG

Basic information

species Zea mays
transcript GRMZM2G064426_T02
intron # 3
splice site 3'
intron type U2

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|60338423|gb|DN205396.1|DN205396
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|31664551|gb|CD573484.1|CD573484
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|31664550|gb|CD573483.1|CD573483
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|71311885|gb|DR792413.1|DR792413
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|29543654|gb|CB604034.1|CB604034
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|71446912|gb|DR827962.1|DR827962
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|60397343|gb|DN230159.1|DN230159
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|71311886|gb|DR792414.1|DR792414
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|149102150|gb|EE287580.2|EE287580
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|149102149|gb|EE188096.2|EE188096
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|60344410|gb|DN211383.1|DN211383
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|71315806|gb|DR794556.1|DR794556
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|149107729|gb|EE189603.2|EE189603
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|71315807|gb|DR794557.1|DR794557
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|76930838|gb|DV172525.1|DV172525
EST:     GACTATATTTGAACCCCTCAAGGTGTATCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GACTATATT-GAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
EST: gi|26557696|gb|CA829931.1|CA829931
EST:     GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGATGG                         AGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG
genomic: GGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGG

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), 48 (downstream exon)
Score: 67

ACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

ACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

ACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 23

ACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtactgatga ... gattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgtagattctgagatataatgaacattgttcttgtttctttgattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG
                                         ctttgat  putative branch site (score: 23)
                                ttcttgtttctttg  CT-rich tract
                 atataatgaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtatgggagtagctcttctcattctccatgctttagctaccaatcttgtagattctgagatataatgaacattgttcttgtttctttgattaacaacAGGGTGATAGTAAGTTAACTTCAAAATCCAGCGATGGCTCCATTAAAAAGGATGCCCTTGGTCATGTGGGAGCAAGTAGCTCAGCTGTACAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - gctacca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg