Sequence
atgc intronic sequence ATGC exonic sequencegtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G27300.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 10
------gtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgata-tcttcatttgcattttcagc-caattaatattaataacaactgactgat--ttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
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gtttgtctctttccattcaatttgtgtggattttttttctccctcttcagtc-attcaattcttgctttccattcttgttcataatgctcatagcttctataccactttcttgttgatatacatacaaattgcagGTTCTTGAATCAGTACTTCCTATTAAAGATGATGAGGTTGTTCTAGGACAATATGAAGGCTATAAAGATGATCCAACTGTGCCTGACAATTCAAACACTC
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 10
gtgattacagttttcttgat-cacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
| || | ||||| | | ||| | | |||| ||| ||| | | | | || | | || || | |||||| | | | || || || | ||||||||| |||| ||| | || || || ||||| ||||| |||||||||||||||||||| |||| |||||| ||||| || || |||| || ||||| |
------------tcaatgttgcacatttatggttacctagtttttgaga--tgagtcacaccat-----gcctctatagatcata-----tgataacactttatgg--ttgctacggaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCC
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
gtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
| | ||| ||||| | | ||| | | |||| ||| ||| | | |||| | | |||| |||||| | | | | || || | ||||||||| |||| ||| | || || | |||||| ||||| |||||||||||||| ||||| |||| |||||| ||||| || || | | |||||||| |
------aaaattt-------cacatttatggttacctagtttttgaga--tgagtcaca---------gcatgcctctatatatcatat-gataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
upper sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
gtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
| | ||||| | | | | || | |||| | | | | | | | | || || ||| | || | | |||| |||||||||||||||| ||| |||| || | ||||| ||||| |||||||||||||| ||||| || | |||||| ||||| ||||| | ||||| || |
-------------------actctcttttagataaggtcctctata---ttttgtgaggtttctgtat-tgtcccatacatgtcgtttcctgtaccacttgat--aattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
aattaatattaataac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG