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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagactgaaaccgaaaacgtcgttctctatctattttgaatgattttgctcctcgcagtggcctcagcaaatgatcttatgtatcgtcgttctcttaatcctggtgcaacag

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 17
GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagactgaaaccgaaaacgtcgttctctatctattttgaatgattttgctcctcgcagtggcctcagcaaatgatcttatgtatcgtcgttctcttaatcctggtgcaacag
||| ||||||||||||||||| ||||| || || || ||||| |||| ||| | ||| || |||||||||||  | || ||||  |||||||||||||||||||  | | | | ||   ||  | |  |   ||            |||  |    |||||||     | ||  | |||         || |||||||||| ||| || | ||||||
GTCAAACGGGGTAACTGGAGACTTTGCTACCATGTGTGAAGATCCTAAAGCAAAAGAATTTATCTTGGGAGAATTAACCAAGACTGGTAAAGAAAAGAAGgtaagta-atttagac---aagtgacaatgcatac---------gcgatcct----ctcgcaga----ttag-gattgac--------tcatcgttctcttgatcttgttacaacag
















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|33096859|gb|CF056819.1|CF056819
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTCGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|86470254|gb|DY236624.1|DY236624
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|33770959|gb|CF273253.1|CF273253
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|211196583|gb|FL038431.1|FL038431
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTCGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|5688735|gb|AI941750.1|AI941750
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|71426982|gb|DR808032.1|DR808032
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|60349126|gb|DN216099.1|DN216099
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|60339626|gb|DN206599.1|DN206599
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|6020548|gb|AW065476.1|AW065476
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGNTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|60358314|gb|DN225287.1|DN225287
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|94473569|gb|EB702527.1|EB702527
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATTTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|74246154|gb|DT654068.1|DT654068
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|74239652|gb|DT647566.1|DT647566
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|16920190|gb|BM074544.1|BM074544
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
EST: gi|71431178|gb|DR812228.1|DR812228
EST:     CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAG                         CTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC
genomic: CGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTC

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), 47 (downstream exon)
Score: 110

GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCAC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 60

GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCAC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 33

GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagac ... ggtgcaacagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGAACGGGGTAACTGGAGAATTTGCCACGATATGCGAAGACCCTAGAGCGAGAGAGTTCATCTTGGGAGAGCTTACAAAGATGGGTAAAGAAAAGAAGgtaataagactgaaaccgaaaacgtcgttctctatctattttgaatgattttgctcctcgcagtggcctcagcaaatgatcttatgtatcgtcgttctcttaatcctggtgcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG