Sequence
atgc intronic sequence ATGC exonic sequence...aaatccttatggcatgggttgggagacaggactttatacatcaggtctatgttatgaagaaagtcatgtgaatattcaccatctttaattatgtttacagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTCAGGTCAAGGCTTAAGCAGTTTTCTGTGATGAATAGATTCAA
Basic information
species | Glycine max |
transcript | GLYMA06G20170.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G18890.1 (Arabidopsis thaliana), 3'ss of exon 3
aaatccttatggcatgggttgggagacaggactttatacatcaggtctatgttatgaagaaagtcatgtgaatattcaccatctttaattatgtttacagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTCAGGTCAAGGCTTAAGCAGTTTTCTGTGATGAATAGATTCAA
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-----------gtgaagttcttgtgtttctgttttctttaatggtcgtagttaccttaatccactctattactaatgattttctttttctcacctttcagCTCACCCATGGATACAGAATGCAAAGAAAGCTCCCAATGTTCCTTTAGGAGATATAGTCAGATCTAGGTTGAAGCAGTTCTCTATGATGAACAGATTCAA
upper sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G74740.1 (Arabidopsis thaliana), 3'ss of exon 3
------aaatccttatggcatgggttgggagacaggactttatacatcaggt-----ctatgtt---------atgaagaaagt--catgtgaa-tattcaccatctttaatta--tgtttacagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTCAGGTCAAGGCTTAAGCAGTTTTCTGTGATGAATAGATTCAA
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gtaataatgctgttcttgtgtcacttgtgaattttgatcttctttgctacttgtttcttgtgttggatttgagatggagaaaatggcatttaaagtgaaaacggtttctgtttccttctttgcagATCACCCTTGGATACAGAATGCAAAGAAAGCTCCAAATGTTCCTTTAGGGGATATTGTTAGGTCAAGGTTGAAGCAATTCTCCATGATGAATAGATTGAA
upper sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 3
aaatccttatggcatgggttgggagacaggact--ttatacatcaggtctatgttatgaagaaa--gtcatgtgaatattcaccat-ctttaattatgttta-cagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTCAGGTCAAGGCTTAAGCAGTTTTCTGTGATGAATAGATTCAA
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------ttatcacctggaaactatttctgtaatcatcctgcaacatggctggtttcttgttaatttgttatactgatttttgcttttcttttctcatctttggcagAACATTCCTGGTTACAGAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTGAGAACAAGGCTCAAGCAGTTCTCTTGCATGAACAGATTCAAMapped 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|14258897|gb|BG881805.1|BG881805EST: GAACAGGTGCTTG AACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAG
genomic: GAACAGGTGCTTGgtaagtcagt ... atgtttacagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatgttatgaagaaagtcatgtgaatattcaccatctttaattatgtttacagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTCAGGTCAAGGCTTAAGCAGTTTTCTGTGATGAATAGATTCAA
ctttaat putative branch site (score: 4)
atctttaattatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatccttatggcatgggttgggagacaggactttatacatcaggtctatgttatgaagaaagtcatgtgaatattcaccatctttaattatgtttacagAACATCCCTGGCTGCAAAATGCAAAGAAAGCTCCAAATGTTCCATTAGGAGATATTGTCAGGTCAAGGCTTAAGCAGTTTTCTGTGATGAATAGATTCAA
- - ccttatg
- - - - - - - -gggttgg
- - - - - - - - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtg