Sequence
atgc intronic sequence ATGC exonic sequence...ttgaaatgttttcacttttgtcttttctgcatgtttgaggatttttaacattgttttatattgtcatctaggtagtgaatatctgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
Basic information
species | Glycine max |
transcript | GLYMA18G07280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 4
ttgaaatgttttcacttttgtcttttctgca--tgtttgaggatttttaacattgttttatattgtcatctaggtagtgaatatctgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
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-------------------gtcagttctgcagtcatttaagtaatgatga-atgttgctggactagagtttttgtactatgatgtaattcattat-ttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGGGAAGCTGAAGTCCCATTCATAAGTTGCTCTGCAAGTGAATTTGTGGAGT
upper sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
---------ttgaaatgttttcacttttgtctttt-ctgcatgtttgaggatttttaacattgttttata----ttgtcatctagg-tagtgaatatctg--ttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
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gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
upper sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 4
----ttgaaatgttttcacttttgtcttttctgcatgtttgaggattttta-acattgttttatattgtcatct----aggtagtgaatatctgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
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gtgagtttaataatgt-agttacaacttatggccatttcttaggtggtttatgcgcaatgtttggttactatctttagaatttatggctttatttccctgttttggtagGTCGGTCTTCCTGGAACAGGGAAAACCCTTCTTGCAAAAGCTGTTGCTGGGGAATCTGATGTTCCATTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
upper sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
-ttgaaatgttttcacttttgtcttttctgcatgtttgaggatttttaacattgttttatattgtcatctaggtagtgaatatc-tgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
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ctaccaaagaacagatacaagtggtttc--cataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacattgttttatattgtcatctaggtagtgaatatctgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
ttatctt CT-rich tract
ttgttttatattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaaatgttttcacttttgtcttttctgcatgtttgaggatttttaacattgttttatattgtcatctaggtagtgaatatctgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg