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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagagttcgttgaattgactttgtgttttagggaagcaaaaaaaaatccttacagattttctcacttatatag

Basic information

species Zea mays
transcript GRMZM2G003734_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003734_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os04g14654.1 (Oryza sativa), 5'ss of exon 20
GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagagttcg---ttgaattgactttgtgttttagggaagcaaaaaaaaatccttacagattttctcacttatatag
||| |||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||  |  | |   ||      |  ||   |||   | |        ||||     | |  || | | | || | |||
GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcatattgtctttatgaaaagcttacttttgtagaattttttttaaaa-----agaatttcttttatttctgtag
















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|67020761|gb|CO449510.1|CO449510
EST:     AAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: AAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|32828198|gb|CD967876.1|CD967876
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTA
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTA
EST: gi|60358866|gb|DN225839.1|DN225839
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|211528665|gb|FL445659.1|FL445659
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|37399448|gb|CF637052.1|CF637052
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|60347475|gb|DN214448.1|DN214448
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|60353462|gb|DN220435.1|DN220435
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|32805346|gb|CD957582.1|CD957582
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTA
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTA
EST: gi|71440283|gb|DR821333.1|DR821333
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|74241259|gb|DT649173.1|DT649173
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|76292770|gb|DV032338.1|DV032338
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
EST: gi|60401370|gb|DN234177.1|DN234177
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGA                         GGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCT

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), 40 (downstream exon)
Score: 64

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 56

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 39

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 51

GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagag ... acttatatagGGTGGTTTGACAATTAATTCATCACCGGAGGTACATCCAGGTTTAGGGGCTCAACAGAGTATTGACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagagttcgttgaattgactttgtgttttagggaagcaaaaaaaaatccttacagattttctcacttatatag

- - - - TTGAAG
- - - -  TGAAGA
- - - - -  AAGAAC