Sequence
atgc intronic sequence ATGC exonic sequencegtttggtgctttgttgatagtcatggttatagaatgtttttttcctagcaaattcatctctgatcaccctctttttacttctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT2G36480.3 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G142168_T01 (Zea mays), 3'ss of exon 4
------------------------------------------gtttggtgctt--tgttgatagtcatggttat--------agaatgtttt---tttcctagcaaattcatctctgatcaccctctttttacttctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
|||| | | || | ||| |||| || ||| || || | || | | | | | ||||| || | |||| || ||||| || | |||||||| ||| |||| ||| || |||| |||||||||||||||| ||||||||||| |||| || | | || |
gttagtatttcattttgcaccatcttcttgacatgggaacagagatggttcctacccctggaaaccatatttatttattgagaggatgacttggacatcacaataactaagttttctttggttgtatttttcatttttgctagGTGTTCTGCAAGGCATATAAACAAGTTGATCCTTCTATACATCATAGCATGAGGCATCTTTTTGGAACATGGAAAGGAGTGTTTCCTCTACCTCCTCTCC
upper sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G07660.1 (Glycine max), 3'ss of exon 1
---gt-ttggtgctttgttgatagtcatggttatagaatgtttttttcctagcaaattcatctctgatc----accctctttttacttctctgaa-----gGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
|| | || || | | | ||| ||| | || ||| | || | | | | ||| ||||| || | | ||| || | || || ||||| || ||||| ||| || | ||| | ||| |||||||||||||||| |||||||||||||||| ||| || || ||||
aatgtactcatgtcctgcacgtctttctcaagatatcttgtctgatttttag-atgcctatttttaagttggtagtttctaattactcctttacattttagGTATTCATCAAAGCATACAGACAGGTTGATCCTTCTGTCCATCAAAGTATGAGGCATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGACCCTTC
upper sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G37610.1 (Glycine max), 3'ss of exon 2
-----------gtttggtgctttgttgatagtcatggttatagaatgtttttttcctagcaaattcatctctgatcaccctctttttactt-ctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
| | | | | || | || ||| | ||| | | | || | | | | || | || | | |||| || |||||||||| || ||||| ||| | | ||||| | |||| |||||||||||||| |||||||||||||||| ||| || | ||||
tgaaatagaaccaatatttccctttgcatttttcgtgtgatatatgttttctaattctatacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAAACAGGTTGATCCTTGTGTTCATTCAAGTATGCAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
upper sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G34910.1 (Glycine max), 3'ss of exon 2
------------gtttggtgctttgttgatagtcatggttatagaatgtttttttcctagcaaattcatctctgatcaccctctttttactt-ctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
| | | | || | || || | ||| | ||| | | | || | | | | || | || | | |||| || ||||||||||| || ||||| ||| | ||||||| | ||| |||||||||||||| |||||||||||||||| ||| || | ||||
tgaaatggaaccatcttttccctttgcatttttcctg-tgatatatgttttctaattctatacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTGCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
upper sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G37600.1 (Glycine max), 3'ss of exon 1
---------gtttggtgctttgttgatagtcatggt-tatagaatgtttttt--tcctagcaaattcatctctgatcaccctctttttactt-ctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
| | || | | | | | ||||||| | | ||| | | || | | | | || | || | | |||| || ||||||||||| || ||||| ||| | | ||||| | ||| |||||||||||||| |||||||||||||||| ||| || | ||||
tgaaatggaaccaaattttccctttgcatttttcctgcaatatatgttttctaattcta-tacacctatttttaactaggtactactactttacattttagGTATTCTGCAAGGCTTACAGACAGGTTGATCCTTGTGTTCATTCAAGTATGAAACATCTTTTTGGAACTTGGAAAGGAGTCTTTCCTCCTCAGTCCCTTC
upper sequence: AT2G36480.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g03880.t01 (Vitis vinifera), 3'ss of exon 2
------gtttggtgctttgt-tgatagtcatggttatagaatgtttttt--tcctagcaa-attcatctctgatc----accctctttttacttctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
| ||| || | | | || |||| | ||| | | | | || || || || | ||| | |||| | |||| |||| || ||||| || || |||||||| ||| |||| ||| || |||||||||||||||||||| ||||||||||| || | || | ||||||
agtagatatcattgcaatgcatctttgctttgtttatctgctatttcctgattccactaatatctcactttggtttgtaacctacctttttttactct--agGTATTCTGCAAGGCATATAGACAAGTTGATCCTTCTATACATCCTGGTATGCGGCATCTTTTTGGAACGTGGAAAGGAGTGTTCCCTCTTGCACCACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttttttcctagcaaattcatctctgatcaccctctttttacttctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
ctctgat putative branch site (score: 4)
tctctgatcaccctct CT-rich tract
tttttactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggtgctttgttgatagtcatggttatagaatgtttttttcctagcaaattcatctctgatcaccctctttttacttctctgaagGTTTTTGTTAAGGCTTACAGGCAAGTTGACCCTCCTATGCATTCTAACATGCGGCATCTTTTTGGAACCTGGAAAGGAGTCTTTCATCCGCAAACACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
