Sequence
atgc intronic sequence ATGC exonic sequence...gagaaggatggagattgtgaagaaccaagttaccatactgtgtcatgttgactttttattgcaagactgtttagtttttcctttccatttcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
Basic information
species | Glycine max |
transcript | GLYMA03G39290.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 3
gagaaggatggagattgtgaagaaccaagt-taccatactgtgtcatgt---tgactttttattgc---aagactgtttagtt-tttcctttccatt-tcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
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---------gccttttttaatcaacctactgtgcttcatactatcatgttcttagcttcctattgccataaaactgtcaaattatcaactatctgttgttttcttgcagGGAAAATGAACAGCTGTCTAAGTACGGGGATACCAAATCTGCTCGCAGTATAATGCTGATTGAGCTCAAAAAACTTATTGAAGCGAACCCCCTTTTCCGG
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 3
gagaaggatggagattgtgaagaaccaagt--taccatactgtgtcatgttgactttttattgcaa--gactgtttagtttttcctttccatttcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
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--tactatcctacagtgttttattccaagtattataattccttagcctgctg-cttctgttttcaatttgtagctcaaaactatcaaataatgttgcttgc-agGGAAAATGAACAGTTGTCTAAGTATGGGGATACTAAATCAGCTCGAAGTATTATGCTGGTTGAGCTAAAAAAACTTATTGAAGCAAACCCCCTTTTCCGG
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
gagaaggatggagattgtgaagaaccaagttaccatactgtgtcatgttgactttttattgcaagactgtttagttttt---cctttccatttcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
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tgaagttgcactacttgttcctttttttaaaacgaaact-tgagatgtgggtgtgtatgtgca--tctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgactttttattgcaagactgtttagtttttcctttccatttcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
tgttgac putative branch site (score: 3)
tttagtttttcctttc putative PPT
actttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaaggatggagattgtgaagaaccaagttaccatactgtgtcatgttgactttttattgcaagactgtttagtttttcctttccatttcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - gatggag
- - - - - - - - - gaagaac
- - - - - - - - - - - - - - - - ccatact
- - - - - - - - - - - - - - - - - - - - - - -tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaga