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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCTCAGGTTGGAGATCAAGgtgcgcctgcccgtcctcactggatctcggtttccaagttgtccttctactactgttcttatcgctttgattttgctctgattttagtttgattttgtttctttggtggtgattag

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 2
CCGCTCAGGTTGGAGATCAAGgtgcgcc---tgcccgtcctcactggatctcggtttccaagttgtccttctactactgttcttatcgct--ttgattttgctctgattttagtttgattttgtttctttggtggtg--attag
||||||||||||||||||||||||||||    || ||  |||   |   |    |   | || | ||  | |  | ||||     | | |  ||  |||||  ||||||||    |  |||||| | |  | |||||  |||||
CCGCTCAGGTTGGAGATCAAGgtgcgccactggctcgggctcggcgagcccgattccgctagatctcggtttgttgctgtctcagttggtggttagttttgtgctgattttgtggttgttttgtctttgggatggtgtgattag
















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|78122343|gb|DV540727.1|DV540727
EST:     TATGCCGCTCAGGTTGGAGATCAAG                         CGAAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGGGGATTTGCCCCCC
genomic: CATGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|18654986|gb|BM499791.1|BM499791
EST:     TGCCGCTCAGGTTGGAGATCAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
genomic: TGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|22489991|gb|BU049914.1|BU049914
EST:     ATGCCGCTCAGGTTGGAGATCAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCNCCCC
genomic: ATGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|18655044|gb|BM499849.1|BM499849
EST:     TGCCGCTCAGG-TGGAGA-CAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGG-GGA-TTGCACCCC
genomic: TGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|18655016|gb|BM499821.1|BM499821
EST:     TGCCGCTCAGG-TGGAGATCAAG                         CGGAAG-TCGCTCAACGG-CGGAGAGGG-CAAGTCGGTGGA-TTGCACCCC
genomic: TGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|89106409|gb|DY576626.1|DY576626
EST:     TGCCGCTCAGGTTGGAGATCAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
genomic: TGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|18654807|gb|BM499612.1|BM499612
EST:     TGCCGCTCAGGGTTGGAGATCAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
genomic: TGCCGCTCAGG-TTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|22489999|gb|BU049922.1|BU049922
EST:     TGCCGCTCAGGTTGGAGATCAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
genomic: TGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC
EST: gi|18649626|gb|BM498445.1|BM498445
EST:     ATGCCGCTCAGG-TGGAGATCAAG                         CGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGG-GGA-TTGCACCCC
genomic: ATGCCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCC

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: 47 (upstream exon), 49 (downstream exon)
Score: 117

CCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCCACGGAGCCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

CCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCCACGGAGCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

CCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCCACGGAGCCATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 169

CCGCTCAGGTTGGAGATCAAGgtgcgcctgc ... tggtgattagCGGAAGTTCGCTCAACGGTCGGAGAGGGTCAAGTCGGTGGATTTGCACCCCACGGAGCCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCTCAGGTTGGAGATCAAGgtgcgcctgcccgtcctcactggatctcggtttccaagttgtccttctactactgttcttatcgctttgattttgctctgattttagtttgattttgtttctttggtggtgattag

- - - -  TTGGAG
- - - - - TGGAGA
- - - - -  GGAGAT
- - - - - - GAGATC
- - - - - -  AGATCA