Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTCTTGAGCGAGCATGGAGATGTCAGCCATGGAGGAAGCCCTCCCCAAGGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaactaagaacaccgagcagctagccatgtctatcttctagcgcgcatgcttgatttggcttggtgtggggttgatctgtccgcggcggcatgcag

Basic information

species Zea mays
transcript GRMZM2G035790_T01
intron # 1
splice site 5'
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|149071140|gb|EE159538.2|EE159538
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211539680|gb|FL070739.1|FL070739
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211533673|gb|FL070722.1|FL070722
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536680|gb|FL070733.1|FL070733
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536681|gb|FL070734.1|FL070734
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAAAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|148968167|gb|EE019456.2|EE019456
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|148931856|gb|EC877314.2|EC877314
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211533666|gb|FL070715.1|FL070715
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAAAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211533667|gb|FL070716.1|FL070716
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536679|gb|FL070732.1|FL070732
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536673|gb|FL070726.1|FL070726
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536675|gb|FL070728.1|FL070728
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211530666|gb|FL070708.1|FL070708
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|149078326|gb|EE167093.2|EE167093
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211530661|gb|FL070703.1|FL070703
EST:     GGCGATGGAGAGGAGGAAGGNAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211527668|gb|FL070695.1|FL070695
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211530656|gb|FL070698.1|FL070698
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536682|gb|FL070735.1|FL070735
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211530657|gb|FL070699.1|FL070699
EST:     CGGATGGAAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: C-GATGG-AGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211530664|gb|FL070706.1|FL070706
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536684|gb|FL070737.1|FL070737
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536683|gb|FL070736.1|FL070736
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|149011546|gb|EE042369.2|EE042369
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211530659|gb|FL070701.1|FL070701
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|149008814|gb|EE041018.2|EE041018
EST:     GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
EST: gi|211536676|gb|FL070729.1|FL070729
EST:     GCGGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCT                         TAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA
genomic: GC-GATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGA

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 2 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 34 (downstream exon)
Score: 13

TCGTCTTGAGCGAGCATGGAGATGTCAGCCATGGAGGAAGCCCTCCCCAAGGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGATCCTGTACCTCACCGAGCGGTATCTCATGACCAACGCCTTTGCCACCGT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 89

TCGTCTTGAGCGAGCATGGAGATGTCAGCCATGGAGGAAGCCCTCCCCAAGGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaacta ... cggcatgcagTAAACGAGATATTCGAGAAGGTGGCCACGTTCGGGCTGTCGGCCAACATGATCCTGTACCTCACCGAGCGGTATCTCATGACCAACGCCTTTGCCACCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTCTTGAGCGAGCATGGAGATGTCAGCCATGGAGGAAGCCCTCCCCAAGGCGATGGAGAGGAGGAAGGGAGGCCTCAGAACCATTCCGTTCATCATCTgtaagaactaagaacaccgagcagctagccatgtctatcttctagcgcgcatgcttgatttggcttggtgtggggttgatctgtccgcggcggcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA