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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCCCGTCCCCTCTGTCCATCGATCACCTTGACCACGTGCCTGTGCCGCAGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcctgatcagtggtgctcttacccgttctgtccggttcgatttgctgatgcggccggctggtttgatcgtttttgggtgcgattgttgtgatt...

Basic information

species Zea mays
transcript GRMZM2G009591_T02
intron # 1
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|211404577|gb|FL228986.1|FL228986
EST:     AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAG                         GATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
genomic: AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
EST: gi|211353622|gb|FL298333.1|FL298333
EST:     AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAG                         GATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
genomic: AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
EST: gi|76920567|gb|DV168236.1|DV168236
EST:     AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAG                         GATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
genomic: AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
EST: gi|211353623|gb|FL298334.1|FL298334
EST:     AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAG                         GATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG
genomic: AGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATG

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: 43 (upstream exon), 49 (downstream exon)
Score: 37

GGCCCCGTCCCCTCTGTCCATCGATCACCTTGACCACGTGCCTGTGCCGCAGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATGGACTGCGGTGCTGGTTCGATTAGTCTAGGCCACAAGGTTTTATGCCGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GGCCCCGTCCCCTCTGTCCATCGATCACCTTGACCACGTGCCTGTGCCGCAGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATGGACTGCGGTGCTGGTTCGATTAGTCTAGGCCACAAGGTTTTATGCCGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GGCCCCGTCCCCTCTGTCCATCGATCACCTTGACCACGTGCCTGTGCCGCAGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATGGACTGCGGTGCTGGTTCGATTAGTCTAGGCCACAAGGTTTTATGCCGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

GGCCCCGTCCCCTCTGTCCATCGATCACCTTGACCACGTGCCTGTGCCGCAGGCCGCAGCCAGGCATCTCCGGCGAATCTGGTTTGAGGCGCGGAGAGAGgtgagtttcc ... tattccacagGATATTTGCATGCGGGACTGATCAATCAAAGCAATGGCAGTAGCGCCCATGGACTGCGGTGCTGGTTCGATTAGTCTAGGCCACAAGGTTTTATGCCGTT