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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttatttttcaaccaagatgttttaggtgaaacagatatgcactagactgaaattttgttatgtatgagttgttctaaggacttcctgtctttatga...

Basic information

species Zea mays
transcript GRMZM2G152319_T01
intron # 4
splice site 5'
intron type U2

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|13558468|gb|BG549824.1|BG549824
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG                         GTCAGGCATTACTATTATCGTCTTGTTCGACG
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACG
EST: gi|18165901|gb|BM335740.1|BM335740
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG                         GTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
EST: gi|71431161|gb|DR812211.1|DR812211
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG                         GTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
EST: gi|93281628|gb|EB673892.1|EB673892
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACCAAGGATCAG                         GTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAAC-AAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
EST: gi|91048426|gb|EB158844.1|EB158844
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCTG                         GTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
EST: gi|89762261|gb|DY689939.1|DY689939
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG                         GTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGT
EST: gi|37418701|gb|CF647022.1|CF647022
EST:     AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG                         GTGAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGG
genomic: AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGG

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), 47 (downstream exon)
Score: 108

AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA


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

AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 89

AACTTCGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAGgtatttattt ... tgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA