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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactcatgagaaaatgtgcatattttaaactggccagcctttttgcacttagagctctaacccaactacaatgtggaaaatttggaactgtcagtctcagtattttcttctgatatttttttgtttcaacttgtag

Basic information

species Zea mays
transcript GRMZM2G451366_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451366_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 5'ss of exon 3
CAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactc--atgagaaaatgtgcatattttaaactggccagcctttttgcacttagagctctaacccaactacaatgtggaaaatttggaactgtcagtctcagtattttcttctgatatttttttgtttcaacttgtag
| || ||||| |||||  | || ||| | |||| |||||||||||| ||||| | |||||||||||||||||| || |||||||| |||||||||||||||||||||    || |||||  | || || ||||    | |  || | || | ||||  | |         | || ||  ||    ||     ||||   ||     |   ||||| | || ||  ||||| |  | ||||||
CGGTCTACTTCGCTTTCCAGGATGACCACTTTGATAACCTGCTGGCGGATATACGTAAAATTGCCTCTTCAGGTCAGCCAGCCTCAGCAACAACAGGAGGgtaatacaagaataagaaatcgagcctactttagcgcgtctggcatgtt-gtactttcaac---------agtataacatg----atactacactgcatgt-----tgccttcttttaat-ttcctttgtctgcatttgtag
















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|211228900|gb|FK998494.1|FK998494
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTCGTGTCCTCAGCAGAGCCTAGA
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGA
EST: gi|91869089|gb|EB400264.1|EB400264
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|211228910|gb|FK998504.1|FK998504
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTANCAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAA-TGTCATCTCCGA
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTA-CAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGA
EST: gi|211226850|gb|FK998490.1|FK998490
EST:     ATCCATAAAATTGCCTCTTCAGGGCAACCAGCCTCTGCAACAACAGGAGG                         TTTTACAA-CTTGTGGTGTCCTCAGCAGAGCCTTAGAAAAGTGTCATCTCC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTT--ACAAACTTGTGGTGTCCTCAGCAGAGCCT-AGAAAAGTGTCATCTCC
EST: gi|148957547|gb|EC903641.2|EC903641
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|101402114|gb|EB822664.1|EB822664
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAAG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAAAAAAGTGTCA
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCA
EST: gi|149084005|gb|EE173399.2|EE173399
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|71326877|gb|DR800096.1|DR800096
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|60339357|gb|DN206330.1|DN206330
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|211228901|gb|FK998495.1|FK998495
EST:     ATCCATAAAATTGCCTCTTCAAGCCAACCAGCCTCTGCAACAACAGGAGG                         T-ACAAACTTGTGGGGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|50335646|gb|CO530772.1|CO530772
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|32921841|gb|CF026653.1|CF026653
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTCGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
EST: gi|71440389|gb|DR821439.1|DR821439
EST:     ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC
genomic: ATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 82

CAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGACCATTTCTAATATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

CAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGACCATTTCTAATATCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

CAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGACCATTTCTAATATCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

CAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGACCATTTCTAATATCCAG