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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttcttttttctttctaaattcctcagatgtaactggcaactagttctctgcacaatagtaatctaggaacattgatcataaggaagagtaatccccttgaactaataacgattttgcatttcag

Basic information

species Zea mays
transcript GRMZM2G409430_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409430_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g54240.2 (Oryza sativa), 5'ss of exon 13
ATACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgt-----tcttttttctttctaa--attcctcagatgta-actggcaactagttctctgcacaatagtaatctaggaacattgatcataaggaagagtaatccccttgaactaata-----acgat-tttgcatttcag-------------------------------
 ||||||||||||||||||  |||||||||| ||||||| |||||||||||||| ||||||||||| ||||| ||||| || ||||| ||||||||||||||     | | |  || | || |  |    ||   |||| ||  |||  |||||||  |   | |||||| | || ||   |||||| |||| |||    |  | |  | |  |||     || || |||   |||  |                               
TTACTGGTTCCAGCAAGCTAATGATAAAGTTCGTCTTGACAGAATTGCTCAACAATTATTCGAACATATTGGCAAGTCGGTCACAGATGATAGTTTTAAGgtgccgatttctgctcctccttatgacctatcttttgtacacctgcagttagttctgagtgtactagtaaccaagaaat-ctgatcaaaagggagatctttttcatcaagcagatatatcgacaatgtttttgtttatgacatttgctaattataattttgtatggtcag
















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|71423078|gb|DR805944.1|DR805944
EST:     AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAG                         CAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGC
genomic: AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGC
EST: gi|211170139|gb|FL323713.1|FL323713
EST:     AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAG                         CAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGC
genomic: AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGC
EST: gi|24766432|gb|CA401586.1|CA401586
EST:     AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAG                         CAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGC
genomic: AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGC
EST: gi|7216514|gb|AW562636.1|AW562636
EST:     AACAGTTATTCGAACACATTGNGAAGTCAGTGACAGACGATAGTTTTAAG                         CAATGGGAAGGGCTGCTCGAGC
genomic: AACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGC

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), 49 (downstream exon)
Score: 87

ATACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGCGGTCTTGAGTTCCTTCACAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 23

ATACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGCGGTCTTGAGTTCCTTCACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 30

ATACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGCGGTCTTGAGTTCCTTCACAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 20

ATACTGGTTCCAGCAAGCTCGTGATAAAGTTTGTCTTGATAGAATTGCTCAACAGTTATTCGAACACATTGGGAAGTCAGTGACAGACGATAGTTTTAAGgttctttttt ... tgcatttcagCAATGGGAAGGGCTGCTCGAGCTCCTTGGTTCTGACATTGGTAGTGCAGGCGGTCTTGAGTTCCTTCACAG