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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgccatttttagaaccttccttaaggttttggtatttgaagtgtacatgtaagtatagaatattcacttttgaggatctggttttcgacgatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG

Basic information

species Zea mays
transcript GRMZM2G435373_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 1
atgccatttttagaaccttccttaaggtttt--ggtatttgaagtgtacatgtaagtatagaatattcac-ttttgaggatctggttttcgacgatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG
    | || |    | ||   | |   ||||  |||  |  |   |  |       | | |  | | ||     | |    |  | ||  || | | ||  |||| ||||| ||||| ||||| |||||||||||||| ||||||||||||||||||||||| |||
---tctttatatctatctgtatgagaattttaaggttctgcagacgacccaccgtctgtgggttgtacatgccctaacagacgtgcttgtgatggtttttcagGTGTTGCACATGGATAGAAATGACTACTATGGAGGGGATTCCACCTCGCTCAACCTTAACCAG

upper sequence: GRMZM2G435373_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 1
-----atgccatttttagaaccttccttaaggttttggtatttgaagtgtacatg-taagtatagaatattcacttttgaggatctggttttcgacgatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG
     || ||||||  |  |    |   |  |    | | || |  |  | ||    |||     | ||  ||  |    ||||    ||||| | | | ||  |||| ||||| ||||| || || |||||||||||||||||||||||||||||||||||||| |||
cccttatcccatttaaaagagtagcggcatagc---gattttgggggatttcacaacaagatctaactaaacagatc---ggatgcacttttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG
















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|149050331|gb|EE048608.2|EE048608
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064222|gb|FL094759.1|FL094759
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|31612099|gb|CD568721.1|CD568721
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064219|gb|FL094756.1|FL094756
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         G-TTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211066961|gb|FL094765.1|FL094765
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064226|gb|FL094763.1|FL094763
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211455108|gb|FL094747.1|FL094747
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|30087663|gb|CB885869.1|CB885869
EST:     GGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064223|gb|FL094760.1|FL094760
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064213|gb|FL094750.1|FL094750
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|149098467|gb|EE184446.2|EE184446
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211066964|gb|FL094768.1|FL094768
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCCCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211066963|gb|FL094767.1|FL094767
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|149103159|gb|EE288530.2|EE288530
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211455107|gb|FL094746.1|FL094746
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064225|gb|FL094762.1|FL094762
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064221|gb|FL094758.1|FL094758
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064220|gb|FL094757.1|FL094757
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064224|gb|FL094761.1|FL094761
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064214|gb|FL094751.1|FL094751
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064212|gb|FL094749.1|FL094749
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211066962|gb|FL094766.1|FL094766
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064215|gb|FL094752.1|FL094752
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GGTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064216|gb|FL094753.1|FL094753
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211455109|gb|FL094748.1|FL094748
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|211064217|gb|FL094754.1|FL094754
EST:     GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAG                         GTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTC

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), 49 (downstream exon)
Score: 544

CAGCCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTGCTTGGCACGGGGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 651

CAGCCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTGCTTGGCACGGGGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 841

CAGCCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTGCTTGGCACGGGGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 348

CAGCCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTGCTTGGCACGGGGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgt ... gatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtaagtatagaatattcacttttgaggatctggttttcgacgatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG
     taagtatagaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgccatttttagaaccttccttaaggttttggtatttgaagtgtacatgtaagtatagaatattcacttttgaggatctggttttcgacgatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
-tgccatt
- - - - - - - - - - - - - -ttttggt
- - - - - - - - - - - - - - - - - - - - - -gtacatg