Sequence
atgc intronic sequence ATGC exonic sequence...ttttatacttctttttctttttattactgtttgttttaaaacattttggggggaaagttcttaagtgtgttattgatatttattttcttgcaatttgtagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA
Basic information
species | Glycine max |
transcript | GLYMA09G40480.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------ttttatacttctttttctttttattactgtttgtttt-----aaaacatt-ttggggggaaagttcttaagtgtgttattgatatttattttcttgcaatttg--tagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA
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gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttatacttctttttctttttatt--actgtttgttttaaaa---cattttggggggaaagttcttaagtgtgttattgatatttattttcttgcaatttgtagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA
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ttctttcttttttttaattttaatttagctatgatttttatactttcaactacctgaaaaagtgtatctcttggtttctgatttttgttttcc-----actgtagGTCAGTTTATTATGCAGCCTCGGATGTGATTATACTCAGATTTATGGTTGAGGTTTGTTGGGCTCCTATGTTGGCAGCTTTCAGTGTTCCACTTGACCAG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 5
-ttttatacttctttttctttttattactgtttgttttaaaacattttggggggaaagttcttaagtgtgttattgatatttattttctt---gcaatttgtagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA
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cttttgttttacatgccctaagttgagttgtgtatgctgg----ctgtgtgagcaaccttttggattttcttctcgatgtttacttgctttggaaaatttgtagGTCAGTTTATTATGCTGCAACAGATGTAGTGATCCTTAGATTCATGATTGAAGTATGCTGGGCTCCCATGTTGGCTGCCTTCAGTGTTCCGCTTGACCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggggggaaagttcttaagtgtgttattgatatttattttcttgcaatttgtagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA
tattgat putative branch site (score: 3)
ttttcttgc putative PPT
ttattgatatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttatacttctttttctttttattactgtttgttttaaaacattttggggggaaagttcttaagtgtgttattgatatttattttcttgcaatttgtagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - -aaaacatt
- - - - - - - - - - - - - - - - - - - - - - - tgggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtt