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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcgatcttttggcgcttgctgtctttgtctagtcctttttttttctgtttctggaactgtcttttagtttgtcaccttacccatctctcgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA

Basic information

species Zea mays
transcript GRMZM2G090338_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090338_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 3'ss of exon 7
cagcgatcttttggcgcttgctgtctttgtctagtcctttttttttctgtttctggaactgtcttttagtttgtcaccttacccatctctcgtatt---ccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCA--GGCTCGCAGCA
    || |||||  ||||    ||     |  |||   |   | |  | |   ||   || |   | ||    | | || ||| |||| | | ||    ||||||||| ||||||||||||||||||||||| ||||||||||||||| ||||||| |||||| |   | ||||||| || | ||  |   |     ||  | | 
agatgaacttttc-cgctaaaggtggaattgcagtagctgaatatagtatagatgttgcttttcatcagc--attatctcacctatcttttgcataaaaccagGGATTTGACAAATTGAAAGAGGTAGTGAACAAGTGGGCAGAGTCAGCATCAGCTGCATGATGGACT-GCTTTCGCTGAACAAGTTGATAACAATTCTGACC-
















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|78114428|gb|DV532817.1|DV532817
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|30087026|gb|CB885234.1|CB885234
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|60339740|gb|DN206713.1|DN206713
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|32808002|gb|CD960236.1|CD960236
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCGTCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|71533637|gb|DR784396.1|DR784396
EST:     GCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: GCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|76015451|gb|DT942621.1|DT942621
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|60349845|gb|DN216818.1|DN216818
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|67030464|gb|CO459213.1|CO459213
EST:     TGGCACACGCCCAG-AAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: TGGCACACGCC-AGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|78114427|gb|DV532816.1|DV532816
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|32802957|gb|CD955193.1|CD955193
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCGTCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|32825466|gb|CD965188.1|CD965188
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCGTCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|71330578|gb|DR802057.1|DR802057
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|60355018|gb|DN221991.1|DN221991
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|31909623|gb|CD651011.1|CD651011
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|47961924|gb|CN844633.1|CN844633
EST:     ATGGCTCACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|13558141|gb|BG549497.1|BG549497
EST:     GAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: GAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|60400045|gb|DN232852.1|DN232852
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|110540151|gb|EE044071.1|EE044071
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|60343246|gb|DN210219.1|DN210219
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|211330976|gb|FL100738.1|FL100738
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACNAACCGAACA                         GGATTCGACAAATTGAAAGA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGA
EST: gi|76917902|gb|DV167065.1|DV167065
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|71448420|gb|DR829470.1|DR829470
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|148947629|gb|EC893109.2|EC893109
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|149085314|gb|EE174820.2|EE174820
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|101384562|gb|EB814326.1|EB814326
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|211113699|gb|FL397738.1|FL397738
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA
EST: gi|32828041|gb|CD967719.1|CD967719
EST:     ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACA                         GGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCGTCA
genomic: ATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCA

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: 47 (upstream exon), 48 (downstream exon)
Score: 102

GAAGCTTGATGACATCGAGAAGGTTTTGGAACCTCTCTTTACCTATTGGAATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 475

GAAGCTTGATGACATCGAGAAGGTTTTGGAACCTCTCTTTACCTATTGGAATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 415

GAAGCTTGATGACATCGAGAAGGTTTTGGAACCTCTCTTTACCTATTGGAATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GAAGCTTGATGACATCGAGAAGGTTTTGGAACCTCTCTTTACCTATTGGAATGGCACACGCCAGGAAGGCGAATCTTTTGGAAGCTTCACAAACCGAACAgtaagtggat ... cgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttctggaactgtcttttagtttgtcaccttacccatctctcgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA
                              accttac  putative branch site (score: 85)
                               ccttacccatctctc  CT-rich tract
                  ttttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcgatcttttggcgcttgctgtctttgtctagtcctttttttttctgtttctggaactgtcttttagtttgtcaccttacccatctctcgtattccagGGATTCGACAAATTGAAAGAGGTAGTGAATAAGTGGGCAGAGTCACCATCAGCCGCATGAAGATTTCGCTTTCGTTGGATAAAATCCCAGGCTCGCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - -tggcgct
- - - - - - - - - tgctgtc