Sequence
atgc intronic sequence ATGC exonic sequencegtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
Basic information
species | Glycine max |
transcript | GLYMA17G18540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G18540.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g02650.1 (Oryza sativa), 3'ss of exon 5
gtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgactttt--ttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
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------------------------gtact-tggcatgttgcttgttctatctgaatccctaatcaaacatccatctt--gtcttgaaacaagatactccgtataatttatttatgtatcatgtcatcagGTGTTCATATCAACAGAGGACTTCTTGCTCTTGGCAATGTCATCAGTGCTCTCGGTGATGAGAAAAAGAGGAAAGAAGGCGCTCATGTTCCTTACCGGGA
upper sequence: GLYMA17G18540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G026218_T02 (Zea mays), 3'ss of exon 5
gtcggtaatacatgattaacttgaatacaatgatatgtatactt-ttgtt--tcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
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--------------------------------gtatgcttgcttcttgtctgtccaaacccttagcctatgtatttatttctatgcc---aaat--taaaggcta---ttttat-acttcgtgacattagGTGTTCACATCAACCGAGGACTTCTCGCTCTCGGCAATGTCATAAGTGCTCTTGGAGATGAGAAAAAAAGAAAAGAAGGTGCTCACGTTCCTTATCGGGA
upper sequence: GLYMA17G18540.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G50240.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataat--tgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
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-----------------------------------------------gttggaaaaacta----agcatcctatttttaatcctcttgagaacgttaactg--acattcttctttcttctctgaaacagGAATTCACATCAATAGGGGACTTCTTGCACTTGGTAATGTTATCAGTGCGCTTGGGGATGAGAAAAGGCGAAAAGAAGGTGCACATGTTCCATACCGTGA
upper sequence: GLYMA17G18540.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g00130.t01 (Vitis vinifera), 3'ss of exon 5
gtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
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----------------------gtaagtagtagtataagccttcttatctcttta-atgaattccatcattctttttgagca--tataaatgatgaaaataag--tttcccccctaattttt--cagGCATTCACATTAATAAGGGGCTTCTTGCACTTGGTAATGTCATCAGTGCACTGGGGGATGAGAAAAAGCGGAAAGAAGGTGTGCATGTTCCTTATCGAGAMapped 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|151399371|gb|EV269242.1|EV269242EST: ATCTGAACGAGCTAAAAGAACAGGTTCTGATGGTGTTCGTTTGAAAGAAG GTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCAC
genomic: ATCTGAACGAGCTAAAAGAACAGGTTCTGATGGTGTTCGTTTGAAAGAAGgtcggtaata ... tttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
atttaat putative branch site (score: 4)
ctttttttt putative PPT
atttaatgactttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatagGTATACACATCAATAAAGGTCTTCTTGCTCTTGGTAATGTCATAAGTGCACTAGGGGATGAGAAAAAGCGAAAGGAGGGTGTACATGTTCCTTATCGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG