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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcacggggatctgggaatcgagggttctactctagggtttccctcggagttttggttgcgtctgtgatctaattgcttctggaatgtgttggatcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG

Basic information

species Zea mays
transcript GRMZM2G131120_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g05650.1 (Oryza sativa), 3'ss of exon 2
gtgagtcacggggatctgggaatcgagggttctactctagggtttccctcggagttttggttgcg--tctgtgatctaattgcttctggaatgtgttggatcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
                  |   |  |||||| |  | | ||||||   |      |  |  ||||  |  | ||||| |||| ||| ||  ||  || |      ||||||||  | |||||||||||||| ||||| || ||||||||||| ||||| |
--------------gtgagtgttttagggttttggt-tggggttttgataccgtctgagcctgcgatttagggatctgattgtttcgggggtggttttgtctcgttgtagGAATACTCAGCCGAGGTTCCAGTTCATCGTTATGAACAGGCGTAACACGG
















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|93282081|gb|EB674345.1|EB674345
EST:     AGCCGCAAGGACGTGGAAGGGTCCCTGTTCGTCGTCAAGAG                         GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
genomic: AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
EST: gi|78086956|gb|DV515349.1|DV515349
EST:     AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG                         GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
genomic: AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
EST: gi|148955226|gb|EC900753.2|EC900753
EST:     AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG                         GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
genomic: AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
EST: gi|211064273|gb|FK983490.1|FK983490
EST:     AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG                         GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
genomic: AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
EST: gi|211064272|gb|FK983489.1|FK983489
EST:     AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG                         GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
genomic: AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG

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), 49 (downstream exon)
Score: 158

AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 189

AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 149

AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 142

AGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAGgtgagtcacg ... tcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggttgcgtctgtgatctaattgcttctggaatgtgttggatcgaatgtagGAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG
                  atctaat  putative branch site (score: 142)
                  atctaatt  TA-rich tract