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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtattgacactatttcctacatgtccaacatgaatattgtacatgatattcacttcatttcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG

Basic information

species Zea mays
transcript GRMZM2G147450_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147450_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 8
------gtcagtattgacactatttcct-----acatgtccaacatgaatattgtacatga-tattcacttcatttcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG
      ||  || | | | || | || |     | |      | |||||| |  ||  | |  |||  |||| |||  |||  ||||||| || || || ||||| ||||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||||||||| |||||||||||||| |
gtcagtgttggtttggtccctttctcttttttgaaacacttcagatgaatctcatatctaaacattagcttccttttattt--agGTGGTCGCATACGATTTTGGAATCAAGCACAATATTTTGAGACGTTTGACGTCATATGGATGCAAGATAACTGTTGTTCCAGCCAATTGGCCTGCTTCTG
















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|22472307|gb|BU036787.1|BU036787
EST:     CTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCAT                         GTGGTTGCCTATGACTTTGGTATCAAGCATAATATTTTGAGACGATTGGCA
genomic: CTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACA
EST: gi|20301382|gb|BQ164325.1|BQ164325
EST:     CTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCAT                         GTGGTTGCCTATGACTTTGGTATCAAGCATAATATTTTGAGACGATCGGCA
genomic: CTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACA
EST: gi|26457213|gb|CA828796.1|CA828796
EST:     CTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCAT                         GTGGTTGCCTATGACTTTGGTATCAAGCATAATATTTTGAGACGATTGGCA
genomic: CTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACA
EST: gi|21760053|gb|BQ635594.1|BQ635594
EST:     AGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCAT                         GCTGGTTGCCTATGCACTTTGGTATCAAGCATAATATTTTGAGACGATTGG
genomic: AGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagG-TGGTTGCCTATG-ACTTTGGTATCAAACATAATATTTTGAGACGATTGA
EST: gi|116818541|gb|EC861576.1|EC861576
EST:     AGAGGGATCAGTC-AGTGAAACTTTTCAT                         GTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACG
genomic: AGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACA

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: 47 (upstream exon), 46 (downstream exon)
Score: 82

TTTGATTAGTGGTGTCACATGTGATGCTCCATATGAATGGTTGGACAAGACTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

TTTGATTAGTGGTGTCACATGTGATGCTCCATATGAATGGTTGGACAAGACTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 95

TTTGATTAGTGGTGTCACATGTGATGCTCCATATGAATGGTTGGACAAGACTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 54

TTTGATTAGTGGTGTCACATGTGATGCTCCATATGAATGGTTGGACAAGACTGACTCAGAATGGGAGTTCAAGAGGGATCAGTCAAGTGAAACTTTTCATgtcagtattg ... tcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctacatgtccaacatgaatattgtacatgatattcacttcatttcttttgtagGTGGTTGCCTATGACTTTGGTATCAAACATAATATTTTGAGACGATTGACATCATATGGATGCAAAATAACAGTTGTTCCAGCAAATTGGCCTGCTTCAG
                                  ttcacttcatttcttt  CT-rich tract
               atgaatatt  TA-rich tract