Sequence
atgc intronic sequence ATGC exonic sequence...ccatgcctaagacttgtgcaaccagtgcaagtttatttatttcctcttatatttgtatatttgacctggaaattttattctcttttgaatatgaatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT
Basic information
species | Glycine max |
transcript | GLYMA02G03800.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G017421_T01 (Zea mays), 3'ss of exon 12
ccatgcctaagacttgtgcaaccagtgcaagtttatttatttcctcttatat-ttgtatatttgacctggaaattttattctcttt-tgaatatgaatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT
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tacagtgtcagcttagtttcaagtctacgtgttcattagattgatgtgatatattgtaaagtgg--ctgataattttatcatttttattcttgtgttgtcagGAGAATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAGTCG
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 11
ccatgcctaagacttgtgcaaccagtgcaagtttatttatttcctcttatat-ttgtatatt--tgacctggaaattttattctcttttgaatatgaatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT
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---agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagtggcagcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 12
ccatgcctaagacttgtgcaaccagtgcaagtttattt--atttcctcttatatttgtatatttgacctggaaattttattctcttttgaatatgaat-atagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT
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-cttagttgggttaaaggccgaacatatgattttactataatttcttcagctactttttaatggaattttt--ttttaattgttctttaaatgttaattatagGAGGATAAGGGATATAATTGTCCAGTGTAAAGGAAGCCTTGTGCTTGAATTGCAGCAGAGATCCATTGAATTTAATTCCATTATTGGGAAGCATCAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatatttgtatatttgacctggaaattttattctcttttgaatatgaatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT
atttgac putative branch site (score: 4)
aaattttattctcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatgcctaagacttgtgcaaccagtgcaagtttatttatttcctcttatatttgtatatttgacctggaaattttattctcttttgaatatgaatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT
-catgcct
- - - - - - - - tgcaacc
- - - - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacctg