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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctacgtttctttcgttattttgatctccagtctgcgcggatgcagatctcatctttctttaattgattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG

Basic information

species Zea mays
transcript GRMZM2G028730_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028730_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g20230.1 (Oryza sativa), 3'ss of exon 1
--------------------gtgagctacgtttctttcgttattttgatctccagtctgc---gcggatgcaga-----tctcatctttctttaattgattga-ttagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG
                      || ||  |     || |       ||||||  | ||||    |   ||| ||     | || ||| | ||| ||| ||||| |||| | |||||||||||||| |||||||| ||||||||||||  |   ||  | ||  |||||
gtcagtgcgttgccgcctccccgatctgggcgcggtttgggtcggagatctctcgcctgctgctcaactgctgactagttttcttctgtatttgattaattgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG
















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|211313558|gb|FL415353.1|FL415353
EST:     GCGTCGGAGACCACATCTTCCGATACTTCNCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211493208|gb|FL377894.1|FL377894
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211366870|gb|FL423721.1|FL423721
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCC-GCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAAGGCCGTCAAGGGGAAGTTTTCTGATGC
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGA-GGCCGTCAAGGGGAAGTTTTCTGATGC
EST: gi|91057201|gb|EB167619.1|EB167619
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GGCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|78109108|gb|DV527525.1|DV527525
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211085621|gb|FL417833.1|FL417833
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|78109107|gb|DV527524.1|DV527524
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTTTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|32913983|gb|CF018795.1|CF018795
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211420632|gb|FL480897.1|FL480897
EST:     GCGTCGGAGACCACWTCTTCCGATACTT-CNCC-CTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|28987245|gb|CB351535.1|CB351535
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|149085223|gb|EE174731.2|EE174731
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|19822283|gb|BQ048307.1|BQ048307
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211443776|gb|FL403729.1|FL403729
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGGAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211105668|gb|FL427080.1|FL427080
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTCTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|32849729|gb|CD989410.1|CD989410
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|93280885|gb|EB673149.1|EB673149
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|37380718|gb|CF627188.1|CF627188
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGTTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211504140|gb|FL387147.1|FL387147
EST:     CGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGST-TGTTTGTTG                         GTCGATAACAAGAAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATG
genomic: CGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTT-GTTGgtgagctacg ... gattgattagGTCGATAACAAGAA-GCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATG
EST: gi|76917162|gb|DV166707.1|DV166707
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG
EST: gi|211041759|gb|FL371260.1|FL371260
EST:     GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTG                         GTCGATAACAAGAAGCTTGAGGAGGC-GTCAAGGGGAAGTTTTCTGATGCG
genomic: GCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCG

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), 46 (downstream exon)
Score: 65

TCACGCCAACCCGCGCTGCGACGACACCGAGCTCCCGCCAGTCGCCAAGCGCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 139

TCACGCCAACCCGCGCTGCGACGACACCGAGCTCCCGCCAGTCGCCAAGCGCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

TCACGCCAACCCGCGCTGCGACGACACCGAGCTCCCGCCAGTCGCCAAGCGCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 123

TCACGCCAACCCGCGCTGCGACGACACCGAGCTCCCGCCAGTCGCCAAGCGCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacg ... gattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatctccagtctgcgcggatgcagatctcatctttctttaattgattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG
                                         aattgat  putative branch site (score: 123)
                                      tttaattgattgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctacgtttctttcgttattttgatctccagtctgcgcggatgcagatctcatctttctttaattgattgattagGTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG