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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttcttctagctaactatgtagcttcatgcatgtaggttatttgtctcctgagtcctgaatctaaaataattcatggatttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 14
gtgggtttcttctagctaactatgtagcttcatgcatgtaggttatttgtctcctgagtcctgaatctaaaataattcatggatttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG
||  ||| ||      |   | ||  | ||||||    | | |   |||| || | |       |  |  ||||||   || ||||||  ||||||| |||||||| |||||||||||||||||||||||||| | | | ||||| |||||||| |||||||||||  | || | | |||||||||||||||
gttagttcctgt--attggttttggcgtttcatgtgcct-gatggcttgtttcttaa-------acatgtaataatctctgaatttctgtagGCTCCTTTGATGACTATAGCTGCAAATGCTGGCATTGATGGTGGTGTGGTCATTGGGAAGCTAATTGAACAAGATAATCTTAATATGGGCTATGATGCAG
















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|33092538|gb|CF052532.1|CF052532
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCAGAAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|211267531|gb|FL446292.1|FL446292
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|67028320|gb|CO457069.1|CO457069
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|5006206|gb|AI712268.1|AI712268
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|31997582|gb|CD661667.1|CD661667
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|76911014|gb|DV164129.1|DV164129
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|113842163|gb|DW968596.1|DW968596
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACC
EST: gi|211181730|gb|FL012621.1|FL012621
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|211184128|gb|FL012625.1|FL012625
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|60394409|gb|DN227279.1|DN227279
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|24764724|gb|CA399887.1|CA399887
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|149072567|gb|EE044214.2|EE044214
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|74242337|gb|DT650251.1|DT650251
EST:     AAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: AAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|71759820|gb|DR957757.1|DR957757
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|78117876|gb|DV536263.1|DV536263
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
EST: gi|31352804|gb|CD437161.1|CD437161
EST:     CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAG                         GCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC
genomic: CAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTC

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: 206

TGGAGTTGCCCTTCTTTATGCCACCAAGGAGCTTGACAAGATTAGCACAGCAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

TGGAGTTGCCCTTCTTTATGCCACCAAGGAGCTTGACAAGATTAGCACAGCAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 58

TGGAGTTGCCCTTCTTTATGCCACCAAGGAGCTTGACAAGATTAGCACAGCAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 71

TGGAGTTGCCCTTCTTTATGCCACCAAGGAGCTTGACAAGATTAGCACAGCAAACGAGGACGAAAAGATTGGAGTTCAAATTATCAAGAATTCTTTGAAGgtgggtttct ... atttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggttatttgtctcctgagtcctgaatctaaaataattcatggatttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG
                           atctaaa  putative branch site (score: 71)
                                              tttctcc  putative PPT
                          aatctaaaataattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtttcttctagctaactatgtagcttcatgcatgtaggttatttgtctcctgagtcctgaatctaaaataattcatggatttctccagGCTCCCTTGATGACCATAGCTGCAAATGCTGGCATTGATGGAGCTATAGTCATAGGGAAGCTGATTGAACAAGAGGACCTCAGTTTGGGCTATGATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA