Sequence
atgc intronic sequence ATGC exonic sequence...gatttaaactagccttctgtgtctgcccgtgctgtttatcttcacagaagtggaaggtttcaagtttatatttctgcatttttgttatgattggatttagGAAGTTGCTGTCAAGAAATTTTTGGACCAGGACTTCTCAGGTGCTGCTTTAGCCGAGTTCAGAAGCGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08720.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 6
gatttaaactagccttctgtgtctgcccgtgctgtttatcttcacagaagtggaaggtttcaagtttatatttctgc-atttttgttatg--attggat--ttagGAAGTTGCTGTCAAGAAATTTTTGGACCAGGACTTCTCAGGTGCTGCTTTAGCCGAGTTCAGAAGCGAA
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----tcaatcatttcccagtttcttaattt-cagaagttttccccaaaacataaggatttctagtctctgtttttctgactgatgatctgctgttgaaatatcagGAGGTTGCTGTGAAGAAATTTTTGGATCAGGATTTTTCAGGTGCTGCATTGTCAGAATTCAAAAGAGAA
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 6
gatttaaactagccttctgtgtctgcccgtgctgtttatcttcacagaagtggaaggtttcaagtttata--tttctg-catttttgttatgattggat--ttagGAAGTTGCTGTCAAGAAATTTTTGGACCAGGACTTCTCAGGTGCTGCTTTAGCCGAGTTCAGAAGCGAA
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---ctcaatcatttcccagtttttaat--ttcaaatgttttccccaaaacataaggatttctagtctctgattttctgactgatgagttgctgttgaaatatcagGAGGTTGCTGTGAAGAAATTTTTGGATCAGGATTTTTCAGGCGCTGCATTATCAGAATTCAAAAGAGAA
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 5
-gatttaaactagccttctgtgtctgcccgtgctgtttatcttcacagaagtggaaggtttcaagtttatatttctgcatttttgttatgattggat-ttagGAAGTTGCTGTCAAGAAATTTTTGGACCAGGACTTCTCAGGTGCTGCTTTAGCCGAGTTCAGAAGCGAA
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tgggttacagt-gccttttttgattgactttact-tccataagattattattgttattattattattattgttataatgttagattttttgtcggacaccagGAGGTTGCTGTGAAGAAGTTCTTGGACCAGGATTTCTCAGGTGCTGCTTTGGCCGAGTTCAAAAGAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaagtggaaggtttcaagtttatatttctgcatttttgttatgattggatttagGAAGTTGCTGTCAAGAAATTTTTGGACCAGGACTTCTCAGGTGCTGCTTTAGCCGAGTTCAGAAGCGAA
tttcaagtttatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatttaaactagccttctgtgtctgcccgtgctgtttatcttcacagaagtggaaggtttcaagtttatatttctgcatttttgttatgattggatttagGAAGTTGCTGTCAAGAAATTTTTGGACCAGGACTTCTCAGGTGCTGCTTTAGCCGAGTTCAGAAGCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -aaactag
- - - - - - - - - - - - - - - - - - - - - cacagaa