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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggctttctatatgcatcaatatttgcctatctgatgagtagaatgctttattttctgccaattttcagttttgataacttttaatctttgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G085000_T03
intron # 6
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|60352714|gb|DN219687.1|DN219687
EST:     GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|60356894|gb|DN223867.1|DN223867
EST:     GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|40303424|gb|CK347811.1|CK347811
EST:     GTGAGGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|148937629|gb|EC881822.2|EC881822
EST:     GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|93282046|gb|EB674310.1|EB674310
EST:     GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|32917029|gb|CF021841.1|CF021841
EST:     GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG

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: 41 (upstream exon), 43 (downstream exon)
Score: 13

GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 44

GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 55

GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 29

GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAgtaagtaaat ... tgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttattttctgccaattttcagttttgataacttttaatctttgttttgtagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
                                         tctttgtttt  CT-rich tract
                         ttttgataacttttaa  TA-rich tract