Sequence
atgc intronic sequence ATGC exonic sequence...agtgcttacaatgatgggtggtcgctcattatgatggtacattcatgtgactcgtgaggatatttggtcactcttttcataatttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 1
agtgcttacaatgatgggtggtc--gctcattatgatggtacattcatgtgactcgtgag-gatatttggtcactcttttcataatttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG---------
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-----------ttaagtgtcattctgtgtatttctacgcaaaattattaggagcaataagtagggtttagtttctgaattgtcgagtcc-tgcctaacttttcccattacagGCTGAAGGAGGTGCAGTAGTAGGGAAACGTGAGAAAGCCAGGCTCAAGGAAATGCAGAAATTGAAGAAGCAGAAAATACAAGAAATATTGGATACACAGA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 1
agtgcttacaatgatgggtggtcgctcattatgatggtac-attcatgtgactcgtgaggatatttggtcactcttttcataatttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG---------
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----------attctgtgtatttctacgcaaaattattaggagcaataagtagggtttagtttctgaattgtcgagattgtcgagtcctgcctaaattttcccattacagGCTGAAGGAGGTGCAGTAGTAGGGAAACGTGAGAAAGCCAGGCTCAAGGAAATGCAGAAATTGAAGAAGCAGAAAATACAAGAAATATTGGATACACAGA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 1
agtgcttacaatgatgggtggtcgctcattatgatggtacattcatgtgactcgtgaggatatttggtcactcttttcataa---tttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG---
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agagtgtgagaagcaacgtgctcgcgaattaacttgtt---tttgtttggctcgcgaatttaaggggaaacctaaagcctaagcgtttgttgtttgactatagGATGGGGATAATGTTGATC---CCGAAATTAGCAAGCGAGAGAAGGCGAGATTAAAAGAAATGCAGAAAATGAAGAAACAGAAGATTCAGGAGATACTGGATG
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 1
-----agtgcttacaatgatgggtggtcgctcattatgatggtacattcatgtgactcgtgaggatatttg--gtcactcttttcataatttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG
|| || | | | | | ||||| | || | | | | | | || |||| || | | |||| | | | || ||||||| | | | | | || |||| || ||||| ||||| ||||| || || ||||||||||||||||||||||| ||||| || ||| |||| || |
aagttgatgaataacgctgtcaggatatgtttaatatgactttttatcctttt-atatatcattatttttgtggtaattgtttttttggtccaa-----at-tgtagGATGGAAATGCTGTGGGTGGCACTGAAATTAGCAAGCGTGAAAAGGCCAGGCTTAAAGAAATGCAGAAGATGAAGAAACAGAAGATCCAGGAAATATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgactcgtgaggatatttggtcactcttttcataatttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG
atttgat putative branch site (score: 5)
ttttcataatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgcttacaatgatgggtggtcgctcattatgatggtacattcatgtgactcgtgaggatatttggtcactcttttcataatttgatggttatatgtagGACGAAGAAGACGAGGAGAAAGCTGAGATCAGCAAACGTGAGAAGGCTAGACTCAAAGAAATGCAGAAGATGAAGAAGCAGAAAATTCAGCAAATCTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC