Sequence
atgc intronic sequence ATGC exonic sequence...caagtatattgttttaatcatcactttttttctgacttcagaattttcttattgttcatgtagtgcttctaagttctaatatctaaatgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
Basic information
species | Glycine max |
transcript | GLYMA06G03300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
caagtatattgttttaatcatcactttttttctgacttcagaattttcttattgttcatgtagtgcttctaagttctaatatctaaatgatac-cgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
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-----------gtatgagcctcattttttttacactctc----ttttgttgtttttt------tgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
upper sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 4
caagtatattgttttaatcatcactttttttctgacttcagaattttcttattgttcatgtagtgcttctaagttctaatatctaa-atgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
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-----gtattgtc--ggctgccaatgatatt-tattagcaaaacctgttt-----ctgagcattgtttg------ataatatgtgatatgacat-gtgcagACACTTCACCGTATGTTTATCATCAATGCCGGTTCTGGTTTTAAGCTACTTTGGGGCACGGTGAAATCGTTTCTTGATCCAAAGACTGTCTCCAAAATAC
upper sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------caagtatattgttttaatcatcacttt--ttttctgacttcagaatt---ttcttattgttca------tgtagtgcttctaagttctaatatctaaatgata-ccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
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gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagtt--gaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttattgttcatgtagtgcttctaagttctaatatctaaatgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
taatatctaaatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagtatattgttttaatcatcactttttttctgacttcagaattttcttattgttcatgtagtgcttctaagttctaatatctaaatgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
- - - - - - - - - - - - - - -ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct