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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattcttctctgcgcattatttctctccagacactgacccatcactactaactgttatattcacctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG

Basic information

species Zea mays
transcript GRMZM2G007915_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007915_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 4
gtattattcttctctgcgcattatttctctccagacactgacccatc-------actactaactgttatattcacctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG
||| | ||||  | |  | || ||| ||||    || |   |||  |        |  | ||   ||| | ||||  || |||||||||||||| |||||||||||||  ||||||||||| ||||||||||||||||| ||||||
gtactgttctagtttctgtataattgctctttgaactcctccccccccccccccccccccaataattaaagtcactcttgtagGTTCATCCTGGGAAACCTTTTGATGCTGATGATGCAGAACATATGCAGTGGATTTACTCAGAG
















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|148940271|gb|EC885047.2|EC885047
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAA
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAA
EST: gi|67018949|gb|CO447698.1|CO447698
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
EST: gi|33099725|gb|CF059685.1|CF059685
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
EST: gi|149099069|gb|EE185089.2|EE185089
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAAACTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
EST: gi|71439588|gb|DR820638.1|DR820638
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
EST: gi|78080951|gb|DV509363.1|DV509363
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGNAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGT
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGT
EST: gi|71440225|gb|DR821275.1|DR821275
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATAT
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATAT
EST: gi|76287587|gb|DV027155.1|DV027155
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAACCTTTTGAT
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGAT
EST: gi|211475001|gb|FK984421.1|FK984421
EST:     GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAG                         GTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG
genomic: GAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 200

TTTTCCTCCACAGGTTAAGTTCCCTTTATGTACTCTCGCCGAGACACCAAGAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

TTTTCCTCCACAGGTTAAGTTCCCTTTATGTACTCTCGCCGAGACACCAAGAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

TTTTCCTCCACAGGTTAAGTTCCCTTTATGTACTCTCGCCGAGACACCAAGAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

TTTTCCTCCACAGGTTAAGTTCCCTTTATGTACTCTCGCCGAGACACCAAGAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgtattattct ... acctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctctccagacactgacccatcactactaactgttatattcacctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG
                            tactaac  putative branch site (score: 120)
                                          ttcaccttttt  putative PPT
                                   tgttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattcttctctgcgcattatttctctccagacactgacccatcactactaactgttatattcacctttttagGTTCATCCTGGAAAACCTTTTGATGGCGATGATGCAGAGCATATGCAGTGGATTTATTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA