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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgctatatagggttgcattgcccaaccccttgcatgagatttgggtcttggtttttagagccttcttttctcggaattgtag

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 18
splice site 5'
intron type U2

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|71328341|gb|DR800800.1|DR800800
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|60345097|gb|DN212070.1|DN212070
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|211010113|gb|FL453006.1|FL453006
EST:     GCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAS
genomic: GCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|148999325|gb|EE036260.2|EE036260
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|37385787|gb|CF630053.1|CF630053
EST:     GAATAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|60356611|gb|DN223584.1|DN223584
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|67015254|gb|CO444003.1|CO444003
EST:     AATAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCCAG                         G-AATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGA
genomic: AACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCC-AGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGA
EST: gi|67022700|gb|CO451449.1|CO451449
EST:     GAATAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGATGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|211145039|gb|FL083882.1|FL083882
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|67018282|gb|CO447031.1|CO447031
EST:     GAATAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|211260918|gb|FL474172.1|FL474172
EST:     AACAGCAATAAGCTAGCTACAATTCGGGTCCCAGCCCGG-ACAGCCCANG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGA
genomic: AACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCA-Ggcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGA
EST: gi|71311110|gb|DR791868.1|DR791868
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|28188021|gb|CB179631.1|CB179631
EST:     GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|211529627|gb|FL478786.1|FL478786
EST:     CAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: CAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|6269998|gb|AW157969.1|AW157969
EST:     GAATAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|149101423|gb|EE187542.2|EE187542
EST:     ACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: ACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
EST: gi|24768245|gb|CA403374.1|CA403374
EST:     GAATAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG
genomic: GAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAG

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: 237

AAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAGCAGTACAGAAGGTCTCATCAATCACAGAGAAACTGTCGCAAATGTCGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

AAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAGCAGTACAGAAGGTCTCATCAATCACAGAGAAACTGTCGCAAATGTCGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

AAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAGCAGTACAGAAGGTCTCATCAATCACAGAGAAACTGTCGCAAATGTCGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

AAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCGGAACAGCCCAGgcaagttcgc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGCAGCTTGCCTGAAACTGGTCGACGAGCAGTACAGAAGGTCTCATCAATCACAGAGAAACTGTCGCAAATGTCGGT