Sequence
atgc intronic sequence ATGC exonic sequence...gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaagaattcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
Basic information
species | Glycine max |
transcript | GLYMA20G36180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 5
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 5
gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaagaattcaagtagtgaaacctaatatatattcct-cacatgttttctatt--cagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
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gaaaagagatggactatataattacattccttgataaataaagtaataaaatgtt---tactttatctgaatttgttgccatgtgtgtgttttctttttgcagCAATTTGAATGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTT
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 5
gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaaga-attcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
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tgctgcaccatg-cctgcccttcacattccttgataaataaagtaataaaatgtttaatttctctgaatttgttcccatgtatgtgtttttctttttgcagCAATTTGAGTGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTT
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 5
--gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaagaattcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
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atgtagtatcatagaccttgttcatatgttcagggtaggaatacctgtcagtattt--attgcttttttttcatctttgcttccttatttttcttgttttagCCATATGAATGGCTAGTGGGAACACAGTACAAGCCAATGGAAATGGTCAAGTCTGATTGGGTTGCTATTAGGAAATCTCCACCATGGGCCATTGATTCGT
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 5
gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaagaattcaagt---agtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
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--tttcacgtttaatagtggaactcttttcatgatgacaatctttgcaaagttttaagccagacttgggtttggtgtttgacatgtttattttttct-tctagCAATATGAATGGCTTGTTGGTTCACAATACAAACCAATGGAGTTGCTAAAGTCTGACTGGGCAGCAATCAGGAAATCTCCACCATGGGCCATTGATTCTTMapped 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|37997477|gb|CF809066.1|CF809066EST: TTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGGCAAATGCTG CAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAA
genomic: TTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgtaatttagt ... ttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagaattcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
tcctcac putative branch site (score: 2)
ttttctattc putative PPT
aaacctaatatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaccttgcaaggatttgtgaggcatttttattgttttaaaaaataaaaagaattcaagtagtgaaacctaatatatattcctcacatgttttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- ccttgca
- - - - - ggatttg
- - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtt