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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagttttaattgttttttttggtcatgtagacctttattcccttgttctttcctttggctagaaaaattgagctagcagtctgcttgtagcaatgttc...

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 5'ss of exon 4
ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagttttaattgttttttttggtcatgtagacctt---tattcccttgttctttcctttggctagaaaaattgagctagcagtctgcttgtagcaatgttc--
||||| |||| |||||||||||||| || ||||| ||||| |||||||||||||| || || ||||||||||| || |||||||||||||  || ||||||||||||| || | ||||||     |||  |||   |   || | | |  |  |   ||||   | |    ||| |      || || ||  |||  || ||   
ATGGTGTCAATAGCTTTGGTGGTCTCGGGGCAACTCTTGTGGACTCACTTGATACACTGTATATAATGGGCCTAAAGGATGAATTTCAGAGGGCCAGAGAgtgagttt-aactattttttc--accatacagaatgtacataatgcttcctcatgcgctttaatttggtccattcacgacagagacttctattag--attttagg
















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|148937008|gb|EC881178.2|EC881178
EST:     GATACCCTATACATAATGGGCCTGAGAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|148934064|gb|EC878076.2|EC878076
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|149108157|gb|EE292504.2|EE292504
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|211506494|gb|FL158303.1|FL158303
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGGTGGCGGAGTCATTAGACTTTGACAAGGGATTATGATGCGAGTGTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGG-TGGCGGAGTCATTAGACTTTGACAAGG-ATTATGATGCGAGTGTT
EST: gi|32929134|gb|CF033946.1|CF033946
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|148930753|gb|EC873061.2|EC873061
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|19058210|gb|BM736877.1|BM736877
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|18964229|gb|BM660885.1|BM660885
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACA-GGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|20300875|gb|BQ163818.1|BQ163818
EST:     TACCCTATACATAATGGGCCTGAAAGATGAATTTTCAGGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: TACCCTATACATAATGGGCCTGAAAGATGAATTT-CAG-AAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|32929269|gb|CF034081.1|CF034081
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|20301029|gb|BQ163972.1|BQ163972
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTG
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTG
EST: gi|13178345|gb|BG349603.1|BG349603
EST:     ATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: ATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|149073799|gb|EE162117.2|EE162117
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|87151942|gb|DY396731.1|DY396731
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|78112348|gb|DV530742.1|DV530742
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|61119084|gb|DN560045.1|DN560045
EST:     GATACCCTATATATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|20300848|gb|BQ163791.1|BQ163791
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTG-CAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|32928842|gb|CF033654.1|CF033654
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|87153018|gb|DY397807.1|DY397807
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|22490422|gb|BU050345.1|BU050345
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|32929345|gb|CF034157.1|CF034157
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTT
EST: gi|18964227|gb|BM660884.1|BM660884
EST:     GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGA                         CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGAT
genomic: GATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGAT

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: 267

ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 407

ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagtttta ... catataacagCTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTATCAACAGCTTTGGTGGTCTTGGAGCAACCCTTGTTGACTCACTTGATACCCTATACATAATGGGCCTGAAAGATGAATTTCAGAAAGCTAGAGAgtgagttttaattgttttttttggtcatgtagacctttattcccttgttctttcctttggctagaaaaattgagctagcagtctgcttgtagcaatgttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaaaa