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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaacttgtcatatcatattcatcggttcatagctagttggtagttgcttgtgcaatgcaatgaattgatttgggtcttgtctcgccag

Basic information

species Zea mays
transcript GRMZM2G328908_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G328908_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 5
CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaacttgtcatatcatattcatc----ggttcatagctagttggtagtt----gcttgtgcaatgcaatgaattgatttgggtcttg-tctcgccag
||||||||||||||||||||||| | |||||||||||||||||| ||||| ||||| ||||||||||||||| | ||||||||||||| |    |  ||   |   || | ||||    | ||      | |||  || ||    |  ||  |    ||  | |||||| |    ||   |||   |||
CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaactgagctgcgatctgcatctccagattttggaatggttattatttcagaggatgaactgctcatggcattgatgttttcctgaatctttgcag
















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|10697534|gb|BE997258.1|BE997258
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|13558898|gb|BG550253.1|BG550253
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|7135782|gb|AW498263.1|AW498263
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|18650231|gb|BM499050.1|BM499050
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|4647713|gb|AI622788.1|AI622788
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|13198231|gb|BG354218.1|BG354218
EST:     ACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: ACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|149040130|gb|EE046781.2|EE046781
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGTGTTGTTTTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|16919363|gb|BM074154.1|BM074154
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|110219083|gb|EC900981.1|EC900981
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGGGTTGTTTTTGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|71772626|gb|DR970554.1|DR970554
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|32849587|gb|CD989268.1|CD989268
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|116820958|gb|EC864226.1|EC864226
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|148934032|gb|EC878040.2|EC878040
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTTTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|13126121|gb|BG316691.1|BG316691
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|148996082|gb|EE035341.2|EE035341
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|13490410|gb|BG517174.1|BG517174
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
EST: gi|13126546|gb|BG317116.1|BG317116
EST:     GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG                         TGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT
genomic: GCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGT

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGTGGAGGGCAAGAGCAGCTGCACCGTCATATCTTCGGCGACGGGGAACCTG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 31

CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaac ... gtctcgccagTGTGGCGTTGTTCTCGTCGGCAGAGAAGGCAAGGCTGTTCCTGCCATACGTGGAGGGCAAGAGCAGCTGCACCGTCATATCTTCGGCGACGGGGAACCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaacttgtcatatcatattcatcggttcatagctagttggtagttgcttgtgcaatgcaatgaattgatttgggtcttgtctcgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC