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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgaagctaactttcaactcggtacctcatttttttttacattgtgatggctctatcatctaaagtttgtgttgtcattgcctattacactacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT

Basic information

species Zea mays
transcript GRMZM2G050658_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050658_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g13870.1 (Oryza sativa), 3'ss of exon 6
taatgaa-gctaactttcaactcggtacct--catttttttttacattgtgatggctctatcatctaaagtttgtgttgtcattgcctattacactacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT
 | || | ||  |  |        || |||   ||| | |  ||   ||   ||||   |  ||||||  ||| |||| |  ||   |  ||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||||  ||||||  ||||| || | ||| ||| |||| ||||||||||| || || ||
-agtgtatgcatatgtatggtagtgttcctacaattatgtcatatggtgctgtggccagactatctaacatttttgtttttgtttatt--tacacaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCACAGTTTTTGATCGTAGAGGTCATGTTGCAAAGCTATGCATAGTATTTCT

upper sequence: GRMZM2G050658_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G06580.1 (Glycine max), 3'ss of exon 4
------------------------------------------taatgaagctaactttcaactcggtacctcatttttttttacattgtgatggctct--atcatctaaagtttgtg----ttgtcattgcctattacactacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT
                                          | ||||    ||| |  |     | |  |  | |     |  | | |||    | |  ||  |  || || | ||    || | |||   || |  |  | | ||||||| ||||||||||| || |||||| ||||||||||| | |||||| | | ||  ||||| ||||  |||||||||| ||| |||||| | || || ||
gtaagtagtagaatatctgtttcaaaaataatggttaggtgttgatgacatgaacct--agtctagaaggttgtctaaccattaactatgaaaattatcaattgtggaatgtgtttggcttttttaatttggtaattaataaatgcagGGTCCTTTGCTGGTCTTGGTTTCCTTTCATGGTACTTATCAGGGAAAGTTAGAGTGTTTGATCGCAGGGGGCATATTGGGAAACTATGCCTAGTCTTGCT
















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|32851915|gb|CD991596.1|CD991596
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|76289417|gb|DV028985.1|DV028985
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|38229749|gb|CF920062.1|CF920062
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|78103665|gb|DV522093.1|DV522093
EST:     GAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|211132096|gb|FL293580.1|FL293580
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|149072273|gb|EE160529.2|EE160529
EST:     GGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|13178326|gb|BG349584.1|BG349584
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|13178327|gb|BG349585.1|BG349585
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|211413509|gb|FK952159.1|FK952159
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|86471570|gb|DY237940.1|DY237940
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
EST: gi|78103666|gb|DV522094.1|DV522094
EST:     GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA
genomic: GAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCA

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: 43 (upstream exon), 49 (downstream exon)
Score: 65

GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 117

GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatg ... actacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatggctctatcatctaaagtttgtgttgtcattgcctattacactacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT
              atctaaa  putative branch site (score: 135)
                                              ctacttc  putative PPT
                 taaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgaagctaactttcaactcggtacctcatttttttttacattgtgatggctctatcatctaaagtttgtgttgtcattgcctattacactacttcagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAACTCACAGCCTTTGACCGCAAAGGGCATATTGCGAAGCTATGCATTGTGTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG