Sequence
atgc intronic sequence ATGC exonic sequence...tccggcacttagaaatgtagaaatttgttttaagtcaagaagttatggatgctgctgctaggttctaaaacgtgttctgagttaattgcatattatgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22260.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22260.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA14G34810.1 (Glycine max), 3'ss of exon 17
-------tccggcacttagaaatgtagaaatttgttttaagtcaagaagttatggatgctgctgctaggttctaa-aacgtgttctgagttaattgcatattatgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
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tacatacttttgtttatggtaacatataaga--gtttttgcatatgctattatgctgtttcctggtgtgctgtagtaatactttttatattacatatcacagATGCAGAGCATCAAAGGAGGAGGCCATCCTCGTCCTTCAAATATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCGGACGATCCCTATGCAT------
upper sequence: AT1G22260.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G01840.1 (Glycine max), 3'ss of exon 17
tccggcacttagaaatgtagaaatttgt-tttaagtcaagaagttatggatgctgctgctaggttctaaaacgtgttctgagttaattgcatatta----tgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
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-----aatggtgacatataagtgtttttgcatatgctatgctgttttctggtgtgctgcaataatactctatatgatttttcttttttgcacatcactgatgcagAGCATCAAAGGAGGAGGCCATCCTCATCCTTTAAACATTGGTGATTTGTTTTCAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGAT-
upper sequence: AT1G22260.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G07980.1 (Glycine max), 3'ss of exon 10
tccggcacttagaaatgtagaaatttgttttaagtcaagaagttatggatgctgctgctaggttctaaaacgtgttctgagttaattgcatatta----tgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT--
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ccatacttttgttaatggtgacatataagt-gtttttgcatatgctg--tgctgtagtaatactctatatgatttttc---ttttttgcacatcactgatgcagagCATCAAAGGAGGAGGCCATCCTCATCCTTCAAACATTGGTGATTTGTTTTTAGAAGGGTCTCTTAATCCATATGCAGAGGATCCCTATGCATTTGATTAG
upper sequence: AT1G22260.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv18s0001g05600.t01 (Vitis vinifera), 3'ss of exon 17
---tccggcacttagaaatgtagaaatttgttttaagtcaagaagttatggatgctgctgctaggttctaaaacgtgttctgagttaattgcatattatgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
| | || || || | | | | |||| | ||| || | || | | |||||| | ||| | || |||||| | || ||| | | || ||||||| || || || ||||||||||| ||||| || |||||||| |||||||| |||||||||||||
actagttgaatataaaagtgaaccattattctttacagtgcaactatatttatttcctttctgcttatcggagtttgttctatttgtattcc---ttgtgcagGAAATTAAGGGAGATAGGCATCTACACCCTTCAAATATAGGCGAGTTATTTTCAGAAGGCTCTCTTAATCCATATGCAGATGATCCTTATGCATTTGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatgctgctgctaggttctaaaacgtgttctgagttaattgcatattatgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
ttaattgcatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccggcacttagaaatgtagaaatttgttttaagtcaagaagttatggatgctgctgctaggttctaaaacgtgttctgagttaattgcatattatgcagGGCACAGGAATGACGAGTCATGCTCGCTCTGCAAATATTGGAGACTTGTTTTCAGAAGGTTCTCTCAACCCATATGCTGATGATCCCTATGCATTTGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - gtagaaa
- - - - - - - - - - - - - - - - - -caagaag
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaac