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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcggttcaatagttctatgacccgttcacaatgttctttataatttgctgttatgctgataattagacaagaaatcttttgccttattctattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA

Basic information

species Zea mays
transcript GRMZM2G023335_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023335_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 3'ss of exon 10
gtttgcggttcaatagttctatgacccgttcacaatgttctttataat----ttgctgttatgctgataattagacaagaaatcttttg----ccttattctattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA
      | ||  | |     || |||| |    ||| |  ||   | |    ||||  || |||| ||  ||| |||| ||| ||| ||    ||||  |   |||| ||||||||| | ||||| ||||| |||||||||||||| || ||||| |||||||| || ||||||||   ||  || |||||||||  ||| ||| |||| |
------gtttgcaca----catcacccttcggaaatatctttaggagtgcacttgcatttctgctaatggttaaacaaaaaaacttatgtgttcctttcttgtttttgcagGTTTCAATATATGGGCACTCGTTAGGAAGTGTTCTATCTTATGACATACTTTGCCACCAAGAATCTTCTTCTGCACCATTTCCAGTAGATTATATGAATA
















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|211031557|gb|FL471477.1|FL471477
EST:     GTACATGAAATTTCTGAAGAGAAATTCCTGGTTGCAGTGGAAAG                         GTTTCATTGGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACT
genomic: GTACATGAAATTTCTGAAGAGAAA-TCCTGGTTACAGTGGAAAGgtttgcggtt ... tattttacagGTTTCATT-GTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACT




















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: 49 (upstream exon), 45 (downstream exon)
Score: 140

GTCTCTAACCAGTTGAACAAGCTGTACATGAAATTTCTGAAGAGAAATCCTGGTTACAGTGGAAAGgtttgcggtt ... tattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 128

GTCTCTAACCAGTTGAACAAGCTGTACATGAAATTTCTGAAGAGAAATCCTGGTTACAGTGGAAAGgtttgcggtt ... tattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

GTCTCTAACCAGTTGAACAAGCTGTACATGAAATTTCTGAAGAGAAATCCTGGTTACAGTGGAAAGgtttgcggtt ... tattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 94

GTCTCTAACCAGTTGAACAAGCTGTACATGAAATTTCTGAAGAGAAATCCTGGTTACAGTGGAAAGgtttgcggtt ... tattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgttatgctgataattagacaagaaatcttttgccttattctattttacagGTTTCATTGTATGGCCACTCATTAGGAAGTGTTCTGTCGTATGATATACTTTGTCATCAAGAATCCCTTTTGGCCCCATTTCCAACAGAGTATCTGAACA
         tgctgat  putative branch site (score: 94)
                              tcttttgccttattct  putative PPT
                                       ttattctattttaca  TA-rich tract