Sequence
atgc intronic sequence ATGC exonic sequence...ttcaccgttttacaatctgtagcaagtaacgattcatagattgtggtttctctcttttcgtcatgactaacgtttttgtctttgaattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G14410.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 1
-----ttcaccgttttacaatctgtagcaagtaacgattcatagattgtggtttctctcttttcgtcatgactaacgtttttgtctttgaattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
|| | || | | | | || || || | || | | | ||| | |||| ||| |||| | ||||||||||||||||| |||||||||||||| |||||||||||| | || |||||| |||| || ||| |||| |||||||| |||| ||| | | |||||
ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggagaaaatgtgtc-----tgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
upper sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G18730.1 (Glycine max), 3'ss of exon 2
ttcaccgttttacaatctgtagcaagtaacgattcatagattgtggtttctctcttttcgt-catgactaacgt---ttttgtctttg-aattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
| || | | | | | ||| | ||| | || | ||| | || | || || | | || ||||||| |||| | ||||||||||||||||| |||||||||||||| |||||||||||| | || |||||| |||| || ||| |||| |||||||| |||| ||| | | |||||
-----tggttcaatttaaggaatgaataatcaaggataaaatgctgaaattctgtgttgttatgtggctgatgcatattctgtcttttcaatttgttgtctgcagTGGGTTTTGTCTTCTAAGGAAATTAACTTCCCTTATCCTTTGGGGTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
upper sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 3'ss of exon 1
-ttcaccgttttacaatctgtagcaagtaac-gattcatagattgtggtttctctcttttcgtcatgactaacgtttttgtctttgaattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
|| ||| | || | | | ||| | || | || || | | | || | | |||| | | ||||| | || |||||||||||||||| |||||||| |||||||| || || |||||| ||||| | || || ||| |||| |||||||| ||||||||| |||| |||| ||
tttttttttttctttacctctctcttatccttgatatctctgtttgagctttgcttcacatggc-taacagatgattttcttctaaaattg-taaaatgtagTGGGTTTTGTCATCAAAGGAAATAAATTTCCCCTACCCACTTGGACTGACTCTGCTTCACATGGTCTTCTCCTCTGTATTGTGCTTTATTCTCACCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttctctcttttcgtcatgactaacgtttttgtctttgaattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
gactaac putative branch site (score: 1)
ttgctct putative PPT
tttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaccgttttacaatctgtagcaagtaacgattcatagattgtggtttctctcttttcgtcatgactaacgtttttgtctttgaattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG
- - - - - - - - - - - caagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttttg
