Sequence
atgc intronic sequence ATGC exonic sequencegttggttcatatttcttctttgatcatgaaagtatctagaggatttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38960.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g52340.1 (Oryza sativa), 3'ss of exon 2
-gttggttcatatttcttctttgatcatgaaagtatctaga---ggatttggaggtgtgttgtgataggtttgaatgcgtttaat-------------agGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
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gactattttatttgttaactttgtgtatgattgcaccaaaatatgacattgaaaataaacactcaaaaaaattcacttgtttatttgctttcttgtttagGTTAAATTGTGGTGTGACTGCCCTTTCTGGCCTGATGATGGAATGTGTCGGCTTAGGGATTGTAGTGTCTGTGAGTGCCCAGAGAATGAGTTTCCTGAGC
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
--------------gttggttcatatttcttctttgatcatgaaagtatctag--aggatttggaggtgtgttgtgataggtttgaatgcgtttaata-gGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
| | || || | || ||| | | || | | || || || | ||| || | || ||||||| |||||||||| ||||| |||||||| |||||||| |||||| | | ||||| || ||||||||||| ||||| || | ||||||||||||
ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 2
---gttg--gttcatatttcttctttgatcatgaaag-tatctagaggatttggaggtgtgt-tgtgataggt---------ttgaatgcgtttaata-gGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
| || | || | || | || ||| | ||| || | || | ||| || || || || ||| || ||||||| |||||||||| ||||| |||||||| |||||||| |||||| | | ||||| || ||||||||||| || | || | |||||||| |||
tgtgatgccaccaaaatactcacattaaaaataaaaaatttctgcagtggccagtggctcatctgttctaagtcacgtgctgttccttgtcttttgtaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGCTCAGAGAATGAGTTCCCCGAAC
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2
--gttggtt-catatttcttctttgatcatgaaagta-------------tctagaggat--ttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
| || || ||| |||| | ||| | | | | || | | | |||| || |||| | ||| |||||| || | |||||||| ||||| || |||||||||||||||||||||||||| | ||||| ||||| |||||||| ||||||||||||||||| |||
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctcatgaatcttctgtgctaaaggtgaa-actttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2
--------------gttggtt---catatttcttctttgatcatgaaagtatctagaggatttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
| | | ||||||| || | || | | || ||| ||| | ||| |||||| || | |||||||| ||||| || |||||||||||||||||||| ||||| | ||||| ||||| |||||||| ||||||| || ||||| |||
tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 2
-----------gttg-gttcatatttcttctttgatcatgaaagtatctagaggatttggaggt-gtgttgtgataggtttgaatgcgttt----aatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
||| | ||| | | || | | | | || | | | || ||| | | || | ||| |||| ||| |||||||||| ||||| || |||| |||||||| ||||||| || | || ||||||||||||||||| || |||| ||||||||||||
ttgtttattctgttatacttcaattgatattgtgttttcgcttatgcttgactgacctatatcccattttctgaagcctgttgatccatttctatggtagGCTAAGTTGTGGTGTGACTGCCCTTTCTGGCTAGATGATGGTATGTGCCACTTGCGGGATTGCAGTGTTTGTGAATGCCCCGAAAATGAGTTCCCTGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtatctagaggatttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
tttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttcatatttcttctttgatcatgaaagtatctagaggatttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG