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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgaaataaatgatgtttaatcttgcttagactgaggcatcttctgtttcttagttcaatttctatgtctgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG

Basic information

species Zea mays
transcript GRMZM2G040247_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 14
gtaactgaa--ataaatgatgtttaatcttgcttagactgaggcatcttctgtttcttagttcaatttctatgtctgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG
|||| |||    |  ||  |||| |||  |  | | ||||| |   ||||||||| ||  ||  |||| | |  | |||| |||||| || |  || ||||||||||| |||||||||||||||||| |||||||||| |||||||||||||||||  ||||||||||  |
gtaattgagctgtgtattctgttcaatactcttgacactgatgttccttctgtttattcattgcatttttgtaaccgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATTGTTAGTTTGGTTCCTGATGGGCTAGAAATACCAAG
















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|211348416|gb|FL045968.1|FL045968
EST:     ATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATG                         GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATT
genomic: ATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATT
EST: gi|71445370|gb|DR826420.1|DR826420
EST:     CAATCCCTCCAGAAGCCTGAAATG                         GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACA-T
genomic: CAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATT
EST: gi|74239642|gb|DT647556.1|DT647556
EST:     ATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATG                         GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATT
genomic: ATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATT

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: 87

GCTGTTGAATTTGTTACGGAACAGCATGATGATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 70

GCTGTTGAATTTGTTACGGAACAGCATGATGATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 122

GCTGTTGAATTTGTTACGGAACAGCATGATGATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 67

GCTGTTGAATTTGTTACGGAACAGCATGATGATGAACTGTGGGAGGAACTGATTAGACAATGCCTCCAGAAGCCTGAAATGgtaactgaaa ... tgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttagactgaggcatcttctgtttcttagttcaatttctatgtctgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG
                                 aatttctat  TA-rich tract