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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacctgctatttggaacattctcgtggatatgaattgttgtgcttagtttttatgataatgtctagccgttaactgttctgttgctttggtagcatatcttcctgaggaaagctgacaaataatattaattgttggatttcag

Basic information

species Zea mays
transcript GRMZM2G081924_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081924_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 6
GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaac----------------------ctgctatttggaacattctcgtg-----gatatgaattgttgtgct----tagtttttatgataatgtctagccgttaactgttctgttgctttggtagcatatcttcctgaggaaagctgacaaataatattaattgttggatttcag
| ||  |||||||||||||||||||||| |||| ||||||||||||||| |||||                        || ||    |||  || | |||     ||| |||| | || || |    |   |||||||||||||  | ||  |    || |    ||   || || | |   ||| |||  |   ||||||| |  |   |    | || ||||||
GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAGgttagcaatatgtgacgggaattgtagaactttgttagacagaaagttattgtgctgaagatctgaaatcttatgttactctctattttatgataatgcttggctatccgatgcttcactgtgctgatatcctggtttcttgacaa---ctgacaagtgcttaca----tcggttttcag
















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|211412951|gb|FL027551.1|FL027551
EST:     GCATTCCATATCCTGAAAAGGAAGAAGTCCGTATCCTTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
EST: gi|19351659|gb|BM896191.1|BM896191
EST:     TTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: TTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
EST: gi|42492027|gb|CK701073.1|CK701073
EST:     GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG                         GACCCTAACTTTTG
genomic: GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTG
EST: gi|76292397|gb|DV031965.1|DV031965
EST:     GCATACCATATCCTGAAAAGGAAGAAGTTGGTATCCTTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
EST: gi|60341483|gb|DN208456.1|DN208456
EST:     TGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: TGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
EST: gi|76292398|gb|DV031966.1|DV031966
EST:     GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
EST: gi|22491227|gb|BU051150.1|BU051150
EST:     GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
EST: gi|87152125|gb|DY396914.1|DY396914
EST:     GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG                         GACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT
genomic: GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCT

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: 259

GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCTGCCACAGACGATGTCCGCTTCCTTCTCAATATCTACGAGAAAATGATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCTGCCACAGACGATGTCCGCTTCCTTCTCAATATCTACGAGAAAATGATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCTGCCACAGACGATGTCCGCTTCCTTCTCAATATCTACGAGAAAATGATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 215

GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacc ... tggatttcagGACCCTAACTTTTGGACAATTAGGCCATTGTCTGATATGATGGTTCGAGCTGCCACAGACGATGTCCGCTTCCTTCTCAATATCTACGAGAAAATGATGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAGgtcagcaacctgctatttggaacattctcgtggatatgaattgttgtgcttagtttttatgataatgtctagccgttaactgttctgttgctttggtagcatatcttcctgaggaaagctgacaaataatattaattgttggatttcag

- - - - - - - -  AAGGAA
- - - - - - - - -  GGAAGA
- - - - - - - - - -  AAGAAG
- - - - - - - - - - - AGAAGT