Sequence
atgc intronic sequence ATGC exonic sequencegttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25760.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
-----------------------------gttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|||| |||| ||| | | | ||||| | | || ||| | ||||| ||||||||||| ||||||||||||||||||||||| || ||||| || || |||||| || | |||||||||||||| |||||||| || || ||| | ||||
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattt--tagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
gtta--tttgttttatttcctggcaactttccttgt-caatcattaacttggtct----atttgt---------tagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|||| |||| || |||| || | ||| | | || || ||| || || | ||| | ||||||||||| |||||||| |||||||||||||| |||||||| || || |||||| || | || || | |||| | ||| |||||||| ||||| ||||
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
---------gttatttgtttta---tttcctggcaact--ttccttgtcaatcattaacttggtctatt--tgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|||| | | |||| | ||| | || | | ||| | | | | | |||||| ||||| |||||||||||||| |||||||| |||||||| ||||| |||||| || | || ||||| || || |||||||| || || ||| | ||||
gtgaactttgttacaacctccaaattttcttaattactgatccccccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 9
-------------------------------------------------gttatttgt-tttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|| ||| | |||| | || ||| ||| || || | ||| | || |||| ||||||||||||||||||| ||||| |||||||| |||||||| || || || || |||| || | ||||||| |||||||| || | ||||| ||||
gttagtgtagttgatgttctgctcacctttttcttactcctactctttttttgtttttatttaaatactcacaaatttt-ttatctgttattc-ttcaatcaattt---agGGAGAGAACAAAGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTCTGTGTGGAATCTGTCCACAACCTTTCCGGAATTTTGTTGAGT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------gttatttgttttatttcc--tggcaact--ttccttgtcaatcattaacttggtctatttgtt-agggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|| |||||||| | || | | || |||| | ||| | || || || ||||||||||||| ||||| ||||| |||||||| |||||||| || || || || || | || | ||||||| |||||||| || | ||||| ||||
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
---gttatttgttttatt--tcctggcaactttccttgtcaatca----ttaactt-----ggtctatttgtta--gggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
||||| || | | || | | | |||| ||| | | ||| || ||||||| |||||| || ||||| || ||||| |||||||| ||||||||||| || ||||||||| | || ||||| ||||||||||| ||||| || ||||| || |
gttattattgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactcttatgaaactttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
---------------gttatttgttttatttcc--tggcaactttccttgtcaatcat-taacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|| | ||||| | | ||| || | | | | || | | | || | | || ||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||||||| | || ||||| ||||| ||||| ||||| || ||||| || |
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgtta--cagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
---------------gttatttgttttatttcc--tggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
|| | ||| | | | ||| || | || ||| | | | | ||||||| || ||||| || ||||| |||||||| |||||||||||||| || |||||| | || ||||| ||||| ||||| ||||| || ||||| || |
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------------------------------gttatttgttttatttcctggc----aactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
||| |||| || || | | |||| || | | |||| | | || | | ||||||||||||| || |||||||||||||||||||||||||| || || || ||| |||| || ||||||||||| ||||| | |||||||| || |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaat--cccatatat-agGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT------
upper sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 9
--------------gttatttgttttatttcctggcaactttccttgtcaatcatt--aacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
| | |||| || | | ||| |||||| | || |||||||||||| ||||| | |||||||||||| ||||||||||| || || |||||| || | || ||||| ||||| || |||||||| |||||||| || |
gttgacagtttccaaacttaaataggattttcttttatgtgattctgtacatcattctgaaccaacagcttctttagGGAGAGAATAAAGGGTACCTTGTTTGCAAAAAGAAGATGGCAACATCTCCAGAAGCTTTGTGTTGCTTTTGTCCTCAGCCTTTTCGGCAGTTTGTTGAAT------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcctggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
cattaac putative branch site (score: 2)
aatcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT