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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctccattctgttttcgttgatagtagtacattatattgttgacaagtgaaaactcgttctgttcctcttgatttgtgtttcaaatttatccagag...

Basic information

species Zea mays
transcript GRMZM2G006937_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006937_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os11g35710.1 (Oryza sativa), 5'ss of exon 17
TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctc-cattctgttttcgttgatagtagtacattatattgttgacaagtgaaaactcgttctgttcctcttgatttgtgtttcaaatttatccagag
 | || || |||||| | ||| | |||||||||||||| ||||| ||||| |||||  |||| ||||||||||| || || |||||||| || ||||    ||| | ||  | |      |||| || |  |    |          |  |||| | ||  | || |    || |||||  |   
ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgcatttaagttttgctgggattctggggttatgttttgtatcgttcgtggagaactgagttcattttagtctgagcaataattttatggaat-

upper sequence: GRMZM2G006937_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g04750.3 (Oryza sativa), 5'ss of exon 11
----------------TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctccattctgttttcgttgatagtagtacattatattgttgacaagtgaaaactcgttctgttcctcttgatttgtgtttcaaatttatccagag--
                 | || ||||||||| | ||  | ||| |||||||||| ||||| ||||| |||||  | || |||||||||||||| || ||||||||  |||||    || | |||    || |   |||||| | |  || |  |||  |   |  |||  ||     |  | ||    | | |  |  |   
TTAATTTGGATGTAAGATGGAGCGAGATCCAGCCCCGCTGCATTGTGCTGCAAAAGAATTAATCAATATGCAGTTAGAAACAGGAGAGTTTCCCCAACAAgtaagtcccatttaagttccattggggata-tgtcttatatcgatt-catggaaaacttgagttcgttattcaactgtaattttatggaatgagacgaacaa

upper sequence: GRMZM2G006937_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g04750.2 (Oryza sativa), 5'ss of exon 12
TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctccattctgttttcgttgatagtagtacattatattgttgacaagtgaaaactcgttctgttcctcttgatttgtgtttcaaatttatccagag--
 | || ||||||||| | ||  | ||| |||||||||| ||||| ||||| |||||  | || |||||||||||||| || ||||||||  |||||    || | |||    || |   |||||| | |  || |  |||  |   |  |||  ||     |  | ||    | | |  |  |   
ATGGAGCGAGATCCAGCCCCGCTGCATTGTGCTGCAAAAGAATTAATCAATATGCAGTTAGAAACAGGAGAGTTTCCCCAACAAgtaagtcccatttaagttccattggggata-tgtcttatatcgatt-catggaaaacttgagttcgttattcaactgtaattttatggaatgagacgaacaa

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|60352032|gb|DN219005.1|DN219005
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|4681216|gb|AI629886.1|AI629886
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|32844726|gb|CD984407.1|CD984407
EST:     CAAAGGAATCGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|32833838|gb|CD973516.1|CD973516
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|33099602|gb|CF059562.1|CF059562
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|211245891|gb|FL430652.1|FL430652
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|32845053|gb|CD984734.1|CD984734
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|211357851|gb|FL385254.1|FL385254
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
EST: gi|148929654|gb|EC876148.2|EC876148
EST:     CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCTTCAGCAA                         GAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC
genomic: CAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTAC

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: 44 (upstream exon), 49 (downstream exon)
Score: 41

TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTACCGCAACTTGTTCCCCATCTGGGCTCTCGGTGAGTACCATCGTGGCCTTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 72

TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTACCGCAACTTGTTCCCCATCTGGGCTCTCGGTGAGTACCATCGTGGCCTTC


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 4

TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTACCGCAACTTGTTCCCCATCTGGGCTCTCGGTGAGTACCATCGTGGCCTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 152

TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctcca ... ttggtgacagGAGCATGTAGGATGCTTCAACTGCAGCCTCTACTTCAATTACCCAAGCTACCGCAACTTGTTCCCCATCTGGGCTCTCGGTGAGTACCATCGTGGCCTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctccattctgttttcgttgatagtagtacattatattgttgacaagtgaaaactcgttctgttcctcttgatttgtgtttcaaatttatccagag

- - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA