Sequence
atgc intronic sequence ATGC exonic sequencegtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05330.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 2
gtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagaca-aaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
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-------atgagttgtg-tctat--caagttaatagtgtgctgaacttatttatttatgcttggtcttgtcgtgcattaaagcc------ttgggacattattttcttacttt--cagGTTTTGTCTGTGACATTGGATGAATGGTCAAGTGATGAAATAGATGCAATGATTGAAGTTGGAGGAAATTCTTCTGCTAATTCAATTTATGAGGCTTATT
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 4
gtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
| || | || | || ||| | | | | || || ||| || ||| || |||||||| | |||||||||||||||||| | ||||| |||||||| || ||| | ||| | ||||| ||| |||| |||||||| ||||||||||||||||||||||||| |
----------------aaagtttttagtttttttcttcagacagttatatttatcaagttaagagtggtgtgaatgctgaactcatttgtttgatag-cattgttttttactctcagGTTTTGTCTGTGACATTGGATGATTGGTCAGAGGATGAAATAGATGCAATGATGGAAGTTGGGGGAAATGCTTCTGCTAATTCAATTTATGAAGCTTATA
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 2
gtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
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---atgagttgtgtttattaagtta-atagtg--tgctgaacttatctatttatgcttggt--cttgtcgtgcattaaaacct-------tgggacattattttcttactta--cagGTTTTATCTGTGACATTGGATGAATGGTCAAGTGATGAAATAGATGCAATGATTGAAGTTGGAGGAAATTCTTCTGCTAATTCAATTTATGAGGCTTATT
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 4
gtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
|||| ||| | || | || ||| ||| | ||| | | || || || || ||| | || ||||| | ||||| |||||||||||| | ||||| |||||||| || ||| | ||| | ||||| ||| |||| ||||||| ||||||||||||||||||||||||| |
------------atttggccta----gtttttttcttcaattggttatgtctatcaagttaagagtggtgcgaatgctgaactaatttgtttgacag-cactgttttttactctcagGTGTTGTCTGTGACATTGGATGATTGGTCAGAGGATGAAATAGATGCAATGATCGAAGTTGGGGGAAATGTTTCTGCTAATTCAATTTATGAAGCTTATA
upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 4
gtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
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-----atatttagtttcttttgcta-gtttgaatttttagtttttcctccattttgtaaattatac----caatataa-------ttcttaaaacaatattattttggactgttcagGTGTTGTCTGTGGCATTGGATGATTGGTCTGATGATGAAATTGATGCCATGGTTGAGGTTGGAGGAAATTCTTCTGCTAATTCAATTTATGAGGCTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
tttctcc CT-rich tract
aaaattagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatatatcttctttgctctattacatattggttgtccatttgttgtctcttttcttcattactcaagacaaaattagatctctttcgttgtgtactcattgtttggtttctccagGTTTTGTCTGTGACACTAGATGAATGGTCAGATGAGGAAGTCGATTCCATGATTGAAATTGGAGGAAATGCGTCTGCTAATTCAATTTATGAAGCTTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC