Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaacctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31360.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 5
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaac-ctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
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--------------------------------------------tga-gcatagctagttgacatatgttttaagc--agttaagcacatgtgtatctagagtctgcgattaccaatttatcattg--taatt----aagt---gttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT
upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 5
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaacctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
||| || | | | | | || | ||| | | | | | | || | || ||| | ||| | || ||| | | ||| ||| ||||||||||||| || ||||| || ||||||||||||||||| ||||| |||||||| | ||||| |||||| || ||||||| ||||| ||| | ||||
-----------------------------------------ctcagctagggttactgtagcactgtagctct--ctctctcactttcaagcacaatg---------gaatcta-tctataattg-tcagctgcaaatgac-agttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT
upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 4
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaacctacttta--tgaatgatca---atttcctatgtttggttt-ctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
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-----------------------------------------------------------gactcacta--tttcctctatccttcaacagtctcagagtttcatagcaatgctgtgttagttgtatgacaatataattcctggttatggtttgcattgcagGAAGCACATTGCTGTAGTCAATGGGGTCATGACTTTCGACCTGACTACAAGAGCCTCAGTATTCTCAAGACACAGTTCCCTCGTGTTCCTATTGTTGCTT
upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaacctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
|| | | | | | | |||| | || || | | | | ||| | | || | | | || || ||| | | |||| || |||| |||||||| ||||| |||||||||||||| ||||| |||||||| |||||||| || | |||| | || || |||||||| | ||||| | || ||||
--------------------------------------------------ctttttcattatgttatctgtttaccatggttttat-tttttgggcatttatatatgaagc----tgcaggactgtgtaatgttaattctttgattgctttacagGAGGCACATTGCTGTAGTCAGTGGGGCCATGACTTTCGCCCAGATTACAAAAATCTTGGCATCTTAAAGACTCAGTTTCCTGATGTTCCAGTAGTTGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacagaaaacctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
tttctttgc CT-rich tract
tttatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaacctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG