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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttccttgccctctccctcctccttttgccccaatcctgtcgcgtagcattagtggtaaatgagctttgtttcttcgctacgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG

Basic information

species Zea mays
transcript GRMZM2G109032_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109032_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g35340.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------gtgcgttccttgccctctccctcctccttttgccccaatcct---gtcgcgtagcattagtggtaaatgagctttgttt--cttcgctacgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG
                                          |    || |||            |  ||||       | ||        | ||  |  | |  ||||||  |    |    ||||    |||  ||||| || ||||| |||||||||||||||||||| || ||||| || ||||||||||||||||||||||| ||||||||||||||||| || ||||||||||
gttcgtctcgcctcctctcttccccccacgaatccctcctgatatcatctttgggtggggggaatttgttttttgtgggttcttgaaatttgaagtctgggggtgaaatgaaatcatctcgaattcgtgttgcgc-tagGTTCTTGAGGTTGGGTGTGGCAACTCGCGGCTCGGGGAGGAGCTGCTGCGGGAGGGCGTCGCCGGCGGCATCACCTGCGTTGACCTCTCGCCCGTCGCCG
















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|76289600|gb|DV029168.1|DV029168
EST:     TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCG                         GTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
genomic: TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
EST: gi|211091483|gb|FK999631.1|FK999631
EST:     TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCG                         GTCCTCGAGGTCGGGTGCGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
genomic: TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
EST: gi|91055797|gb|EB166215.1|EB166215
EST:     TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCG                         GTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
genomic: TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
EST: gi|211226341|gb|FL315377.1|FL315377
EST:     TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCG                         GTCCTCGAGGTCGGGTGCGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
genomic: TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
EST: gi|71770180|gb|DR968117.1|DR968117
EST:     TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCG                         GTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
genomic: TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
EST: gi|211091484|gb|FK999632.1|FK999632
EST:     TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCG                         GTCCTCGAGGTCGGGTGCGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG
genomic: TCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGG

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), 39 (downstream exon)
Score: 34

GGACGCGCGGTTCGGGAAGGAGGAGCACTACGAGTGGTTCAAGGACTTCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 10

GGACGCGCGGTTCGGGAAGGAGGAGCACTACGAGTGGTTCAAGGACTTCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG


Block sizes: 38 (upstream exon), 42 (downstream exon)
Score: 9

GGACGCGCGGTTCGGGAAGGAGGAGCACTACGAGTGGTTCAAGGACTTCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG


Block sizes: 44 (upstream exon), 31 (downstream exon)
Score: 6

GGACGCGCGGTTCGGGAAGGAGGAGCACTACGAGTGGTTCAAGGACTTCTCGCACTTCCGCCACCTCCTCGCGCCGCTCCTCTCCCCGTCCCTCTCGgtgcgttcct ... acgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgtcgcgtagcattagtggtaaatgagctttgtttcttcgctacgcgtgtagGTCCTCGAGGTCGGGTGTGGCAACTCGCGGCTTGGCGAGGATCTCCTGCGGGAGGGCGTCGCCGGCGGAATCACCTGCGTTGACCTGTCCCCCGTCGCCG
                      taaatga  TA-rich tract