Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgctggttgtcctcttctttactttattttttctctcctgctctcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55930.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
---------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctc---tcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
| || || || || ||| | | || || || | || | | | || | | || | | ||||| ||||||||||||||||| || || || |||||||||||||| ||||||||||| || ||||||
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
---------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctc---tcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
| || | || || ||| | | || | || | || ||| || || | | ||| | | ||||| ||||| || |||||||| || || || |||||||||||||||||||||||||| || ||||||
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 10
------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctct----cttgaaaggttgtctaatttctctccatg--cagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
|||| || | || ||||| |||||| | | ||| | | | || || || ||| ||| ||||||||||| || ||||||||||| || || ||||| |||||||| || ||||| || ||||||||
atattatgagatttatgccactatccaacatcctctttgtgcacttttttatattctgtgtcagaaccttatttcttccttatcttttctgtatgaacagATAGTAACCCTGGAAGATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAA
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 12
----------gtatgttgctggttgtcctctt--------ctttactttattttttctctcctgctctcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
| | | | || ||| | || | ||||||| | | ||| || | | | | | ||| | || || || |||||||| || |||||||||||||| ||||| ||||||||||| ||||| |||
ttgtaagggggattaattttaattcaactccaagttgaggttgtagtaaattttttgttttgtgcaatcaatacaaatactgatgaacacagaattacagGTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------gtatgttgctggttgtcctc--ttctttactttattttttctctcctgctctc--ttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
|| | || ||| | | ||| | | | | || | | | | | || || | | || || | ||||| || |||||||| || |||||||||||||| || || || |||||||| |||||||||
acttcaattcaactttaaaattaaggctgtgttgaatcatttgatatttgtaatcaatacaaataccgatgctaacaaagttgcaccatgcgttatttagGTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------------------------------------------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctctcttgaaaggttgtctaattt--ctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
| || ||| | | | | | || | || || || | | | | | | ||| | || || | ||||| || || ||||| |||||||||||||| ||||||||||| ||||| |||
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ38618 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgctggttgtcctcttctttactttattttttctctcctgctctcttgaaaggttgtctaatttctctccat-gcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
||| || | | ||| | ||| || || |||| || || |||||| ||||| || |||||||| || || ||||||||||| ||||| ||||| ||||||||||| |||
------------------------gtacgtt-tcatatcttcgtagttcttttcgggagta---taatacacttctattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ31527 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgctggttgtcctcttctttactttattttttctctcctgctctcttgaaaggttgtctaatttctctccat-gcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
| | || | | || | || |||| || || |||||| ||||| || |||||||| || || ||||||||||| ||||| ||||| ||||||||||| |||
----------------------------------gtacgtttcatagttcttttcggga--gtataatacacttctattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttattttttctctcctgctctcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
gtctaat putative branch site (score: 3)
tctaatttctctcc CT-rich tract
ttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgctggttgtcctcttctttactttattttttctctcctgctctcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA