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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaacaagtaatattgtttgttatgaattatgcagcctatctcttttagttaaaatatttcatctgtattttgtggcaaattaaattcatggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 3
atgaacaagtaatattgtttgttatgaattatgcagcct--atctcttttagttaaaat-atttcatctgtat--------tttgtggcaaattaaatt-catggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG
            | |   ||   |||| ||   ||  ||  ||||||| | | || | | | ||  |  || |        | ||| || |||||  || ||| |  || |||||||||||||||||||| || || ||||| ||| |||||||||||||||| ||||||
------------tttgcctttacatgagttgcacatactgtatctcttgtggctatattcacttgctacgtgtcaatgacttctgtagctaattatgtttcatcgagtgtagATATGGGGATGGGGAGCCTACCGACAATGCTGCAAGATTCTACAAATGGTTCACTGAG
















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|148941319|gb|EC886225.2|EC886225
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|22472411|gb|BU036891.1|BU036891
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|148961269|gb|EE011991.2|EE011991
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACCAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|26558402|gb|CA830637.1|CA830637
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|22541992|gb|BU092430.1|BU092430
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|211095653|gb|FK967022.1|FK967022
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|211098118|gb|FK967027.1|FK967027
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGG-ATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGT
EST: gi|148940766|gb|EC885587.2|EC885587
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|148970820|gb|EE021584.2|EE021584
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
EST: gi|19437265|gb|BM953675.1|BM953675
EST:     TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTCTTCCTAGCAAC                         ATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT
genomic: TACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTT

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: 337

GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 567

GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 491

GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 874

GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAACgtgagccccc ... tggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagttaaaatatttcatctgtattttgtggcaaattaaattcatggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG
     ttaaaatatttcatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaacaagtaatattgtttgttatgaattatgcagcctatctcttttagttaaaatatttcatctgtattttgtggcaaattaaattcatggtatgcagATATGGGGATGGGGAGCCAACTGATAATGCAGCACGATTCTACAAATGGTTTACTGAG

- gaacaag
- - - - - - - -tgtttgt
- - - - - - - - - - - - - - - -tgcagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattt