Sequence
atgc intronic sequence ATGC exonic sequencegtaaacatgtgactataagaaattattttgtgctttcagttagatcagttgatatatatactttatatgttacccttttctcattgtaaatgtgtaaatccctaatggtattattctgttagGTTGTTCCCTTGGCTTCTATGTTGACTCCTAACCAGTTTGAGGCAGAGAAGTTAACAGGACTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G37850.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 6
----------------------------------gtaaacatgtgactataagaaattattttgt------gctttcagttagatcagttgatata--tatactttatatgt---tacccttttctcatt------gtaaat-----gtgtaaatccct-aatggtat-tattctgttagGTTGTTCCCTTGGCTTCTATGTTGACTCCTAACCAGTTTGAGGCAGAGAAGTTAACAGGACTAAG-
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tatgactgaagtgaactattctatgccttcacctataattgaa-gattatattttattgcttagttaacagggtcctatttttataggatgatacaggcatacttcccttttgtgtatcctatttttatttgagaagtatattcctagtgttagcatctgagtaacacacattttggcaggTTGTTCCAGTAGCTTCAATGTTGACTCCCAACCAGTTTGAAGCAGAACTACTGACAGGCTTTAGG
upper sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 6
gtaaacatgtgactataagaaattattttgtgctttcagttagatcagttgatatatatactttatatgttacccttttctcattgtaaatgtgtaaatccctaatggtattattct--gttagGTTGTTCCCTTGGCTTCTATGTTGACTCCTAACCAGTTTGAGGCAGAGAAGTTAACAGGACTAAG
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-----------acttgaataaataattgc---cattgagtttgatca--tgaattttgt-ctatctgtattattatttcct-------gatgcaaagatcactagctagactttttatggttagGTTGTTCCAGTTGCTTCAATGTTGACTCCTAATCAGTTTGAAGCAGAACTACTAACTGGGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttacccttttctcattgtaaatgtgtaaatccctaatggtattattctgttagGTTGTTCCCTTGGCTTCTATGTTGACTCCTAACCAGTTTGAGGCAGAGAAGTTAACAGGACTAAG
ccctaat putative branch site (score: 3)
ttattct putative PPT
attgtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacatgtgactataagaaattattttgtgctttcagttagatcagttgatatatatactttatatgttacccttttctcattgtaaatgtgtaaatccctaatggtattattctgttagGTTGTTCCCTTGGCTTCTATGTTGACTCCTAACCAGTTTGAGGCAGAGAAGTTAACAGGACTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT