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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgagccacccgcaaaaaaaaaaggccctagttttttttatccccgtaggaggacgtgctgacgaatttttgtgtgcttttcttatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 1
--------gtaccgagccacccgcaaaaaaaaaaggccctagttttttttatccccgtaggaggacgtgctgacgaatttttgtgtgcttttcttatgt-----tatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC
        |  |   ||| ||| | |||    |      |  || |||       |  || |     |  ||      ||    |  ||     | |||     |  || |||||||||||||||||||||||||| ||||| ||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||
gtgcgtgcgcccgccgccgccctccaaaccctagcttaatgcttgtttcccgattctaagtactggattttggtttgcttgctcgccctcactctgtgtgtgtgtgcagGGATTTGAACGAGATACTGGATTTGTACGAGAAGGGGGAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCGCTGCACCTCGGCCATCTC
















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|67015552|gb|CO444301.1|CO444301
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|148959767|gb|EC905658.2|EC905658
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|67037924|gb|CO464466.1|CO464466
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|149010069|gb|EE041876.2|EE041876
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|71305908|gb|DR789081.1|DR789081
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|148935574|gb|EC879617.2|EC879617
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|211230962|gb|FL341122.1|FL341122
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|149105517|gb|EE291042.2|EE291042
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|91049846|gb|EB160264.1|EB160264
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|149073834|gb|EE162156.2|EE162156
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|67014073|gb|CO442822.1|CO442822
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
EST: gi|148973279|gb|EE024361.2|EE024361
EST:     GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCG                         TGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT
genomic: GCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCT

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), 49 (downstream exon)
Score: 174

GCTGCCAGCGCATCGACGACGCGCTCGTGGACCGCATCGCACGCCTCACCGCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

GCTGCCAGCGCATCGACGACGCGCTCGTGGACCGCATCGCACGCCTCACCGCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GCTGCCAGCGCATCGACGACGCGCTCGTGGACCGCATCGCACGCCTCACCGCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GCTGCCAGCGCATCGACGACGCGCTCGTGGACCGCATCGCACGCCTCACCGCCCGACCACCGCACTGCTTCCTCCGCCGAGGCCTCTTCTTCGCCCACCGgtaccgagcc ... tatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccccgtaggaggacgtgctgacgaatttttgtgtgcttttcttatgttatagTGATTTGAACGAGATACTGGATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTC
                  tgctgac  putative branch site (score: 148)
                                    tgcttttctt  putative PPT
                                       ttttcttatgttata  TA-rich tract