Sequence
atgc intronic sequence ATGC exonic sequencegtatatgttccatattcaagcaaagaatcctctgtgaacatgttgtctataatgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 11
gtatatgttccatattcaagcaaagaatcctctgtgaacatgttgtctataatgtatg-tttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
| | || | | | | | |||| | | | | || | |||| | | | | | | | | ||||| ||| ||||||||||||||| ||||| |||||||| |||||| | || ||||| ||||| || | | ||| | |||||||||||| | || |||||| | || ||||
attttcatttactttcctgtgttggga----ctgtacaactaatcttaatgct-tatgctcttctgcttgacttagctttttcgtttctgtgctttaaaat---gcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 11
gtatatgttccatattcaagcaaagaatcctctgtgaacatgttgtctataatgt--atgtttgtaacaccagtctgaaactacaacatcacactttacaatttt----gcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
||| | |||| ||| | | |||| | ||| || | || | || | | | |||| ||||||||||||||| ||||| |||||||| |||||| | || ||||| ||||| || | | ||| | |||||||||||| | || |||||| | || ||||
-------------attttcatttactttcctgtgttgggactgtacaactaatcttaatgcttatgctcttctgcttgacttagctttttcgtttctgtgcttttaaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------------gtatatgttccatattcaagcaaagaatcc------tctgtgaacatgttgtctataatgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
| ||| | ||| | ||||| | | | | |||| | | | || || || | ||| | || |||| | ||||||||||||||| ||||| ||||||||||||||| | || ||||||||||| || ||| | || ||||| ||||| ||| | | |||||| |||||| | |
gttttgtatataagatatagccatcaaatattttagttgtgctctttcatcaacaaatttaacctagacaatcatctttgtggagaatgatggataaaggataaaagagtttgaaatgtttttaggtttgttctttttcttggtcaattaggctgtcatgtttaaagtgtcacgatctgttttatg---tggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------------------gtatatgttccatattcaag----caaagaatc----ctctgtgaacatgttgtctataatgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
| | | || | ||| || |||| || | | |||| | | | || || | || | ||| | || |||| | ||||||||||||||| ||||| ||||||||||||||| | || ||||||||||| || ||| | || ||||| ||||| ||| | | |||||| |||||| | |
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatg---tggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
-------------------------------------------gtatatgttccatattca-agcaaagaatcctctgtgaacatgttgtcta--------taatgta----tgtttgtaacaccagtctgaaactacaacatcacactttacaatt----ttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
| || | |||||| || | || |||| | ||| | | ||| |||||| | ||| || | || || || | | || | ||||||||||||||| ||||| |||||||||||||| |||| ||||||||||| || ||||| || || || ||||| ||| | | ||| || || ||| |||
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 11
-------------------------------------------gtatatgttccatattca-agcaaagaatcctctgtgaacatgttgtcta--------taatgtatgtttgtaacaccagtctgaaac------tacaacatcacactttaca--attttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
| || | | ||||| || | || |||| | ||| | | |||| ||||| || | | | || || || | | | || | ||||||||||||||| |||| |||||||||||||| ||||| ||||||||||| || ||||| || || || ||| | ||| | | ||| || || ||| | |
gtttcttgataagatgttgctatctgggaattttctcttgcttttttagctacttcattcacagagattcattttctggttgtttactgtttgcctttaggtgatgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttatgtggcagAGTGTTCCTGTGCAAGTTGGGCAAACTCCTCCTTTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGTTGAATGCCTTTGAATCATTAGAATTGT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 11
--gtatatgttccatattcaagcaaagaatc-ctctgtgaacatgttgtctataatgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
| | || |||| ||| || | || || | | | | | | ||| | |||| | || | | || | | ||||||||||||||||| | ||| | ||||| ||||| || ||| ||||||| ||||| || ||| | |||||||| ||||||||| ||| |||||| |||||| |||
cttcctttattttttatttttttaaaaaaccattccctggaattttggggtgggaaagatgcta-----accactttgt-----cttcttctggtgtctaatttttgcagAGTGTTCCTATGCAATCTGGGCAGACTCCACCTTTGCTACAGTACTTTGGAACACTTCTAACTAGAGGAAAGCTCAATGCATTTGAGTCATTGGAATTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
ttgtaac putative branch site (score: 2)
tttacaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgttccatattcaagcaaagaatcctctgtgaacatgttgtctataatgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA