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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgcaaagagaaaatttgagagattagtttctggtcagttgatgttgaatttgatatatcttttggtatttattccctcatctcgtcttaaaaacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGTTCTCGATTTGGTTGGCTAGTGCAGAAGACTATGGGATTAGTGTCAAAAT

Basic information

species Zea mays
transcript GRMZM2G429241_T01
intron # 10
splice site 3'
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|67034922|gb|CO463455.1|CO463455
EST:     CACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAG                         GGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGT
genomic: CACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAGgtacttgcaa ... aacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGT
EST: gi|5343001|gb|AI795306.1|AI795306
EST:     CACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAG                         GGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGT
genomic: CACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAGgtacttgcaa ... aacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGT

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), 48 (downstream exon)
Score: 373

GTCAATGACTGAGATAGCAGAGGATAGTGGTGGCACTGGCAGGAAAATTGCACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAGgtacttgcaa ... aacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGTTCTCGATTTGGTTGGCTAGTGCAGAAGACTATGGGATTAGTGTCAAAAT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 191

GTCAATGACTGAGATAGCAGAGGATAGTGGTGGCACTGGCAGGAAAATTGCACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAGgtacttgcaa ... aacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGTTCTCGATTTGGTTGGCTAGTGCAGAAGACTATGGGATTAGTGTCAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GTCAATGACTGAGATAGCAGAGGATAGTGGTGGCACTGGCAGGAAAATTGCACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAGgtacttgcaa ... aacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGTTCTCGATTTGGTTGGCTAGTGCAGAAGACTATGGGATTAGTGTCAAAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 423

GTCAATGACTGAGATAGCAGAGGATAGTGGTGGCACTGGCAGGAAAATTGCACACAACAGAAGTGTTTCTGAGCCGGACTTTGGTAGATCATCCAAACAGgtacttgcaa ... aacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGTTCTCGATTTGGTTGGCTAGTGCAGAAGACTATGGGATTAGTGTCAAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgatatatcttttggtatttattccctcatctcgtcttaaaaacctaacagGGTGCTGGTGGATCAGATGGTACACAGAGCAGTGCATCAGGATCCAGCAGTTCTCGATTTGGTTGGCTAGTGCAGAAGACTATGGGATTAGTGTCAAAAT
 atttgat  putative branch site (score: 423)
      atatatcttttggtat  TA-rich tract