Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatctctttcctactaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13070.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
-----------gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatct--ctttcctactaat-ttgt--ttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
| | | ||| | | ||||| | ||| | || ||| | ||| | | || || | || ||| | ||||| ||||||||||||||||| || || || |||||||||||||| ||||||||||| || || ||
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaacagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
----------gtatgtgccgctct-tcttttgtgcttctttactctctctcttccacagttagctaatct--ctttcctactaatttgtttct---gcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
| || || | | | ||||| | ||| | | ||| | ||||| | || || | |||| | ||||| ||||| || |||||||| || || || |||||||||||||| ||||||||||| || || ||
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 10
----------gtatgtgccgctcttc--ttttgtgcttctttactctctctcttccacagttag---ctaatctctttccta-ctaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
| | |||| || | | | | || | ||| | | | | || || || || |||| | || || | ||| | ||||||||||| || ||||||||||| || || ||||| |||||||| || ||||| || ||||| |||
atattatgagatttatgccactatccaacatcctctttgtgcacttttttatattctgtgtcagaaccttatttcttccttatcttttctgtatgaacagATAGTAACCCTGGAAGATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAA
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatctctttcctactaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
| | | ||| || | | || | | | || | | | | | | | | || | ||| | || || || |||||||| || |||||||||||||| ||||||||||||||||| ||||||||
ttgtaagggggattaattttaattcaactccaagttgaggttgtagtaaattttttgttttgt-gcaatcaatacaaatactgatgaacacagaattacagGTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 3'ss of exon 13
--gtatgtgccgctcttcttttgtgcttcttt---actctctctcttccacagttag--ctaatctctttccta-ctaatttgt--------ttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
| | | || | || | | | | | | | | | | | | ||| | | ||| | || ||| || | || | ||||| || |||||||| || |||||||||||||| || ||||| |||||||| ||||| ||
acttcaattcaactttaaaattaaggctgtgttgaatcatttgatatttgtaatcaatacaaataccgatgctaacaaagttgcaccatgcgttatttagGTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------------------------------gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatc-tctttcctactaatttgtt----tctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
||| | | ||| | | || | | || || | | | || || | | | | | | || | || ||| | || || | ||||| || || ||||| |||||||||||||||||||||||||| ||||| ||
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccct-gctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ38618 (Selaginella moellendorffii), 3'ss of exon 10
gtatgtgccgctcttcttttgtgcttctttac-tctctctcttccacagttagctaatctctttcctactaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
||| | || | | |||| || || || || | | ||||||| ||||| || |||||||| || || ||||||||||| ||||||||||| ||||||||||||||
----------------------------gtacgtttcatatcttcgtagtt--cttttcgggagtataatacacttctattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ31527 (Selaginella moellendorffii), 3'ss of exon 10
gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatctctttcctactaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
| || || |||| || || || || | | ||||||| ||||| || |||||||| || || ||||||||||| ||||||||||| ||||||||||||||
-----------------------------------gtacgtttcatagtt--cttttcgggagtataatacacttctattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactctctctcttccacagttagctaatctctttcctactaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
tactaat putative branch site (score: 1)
tttgtttct CT-rich tract
taatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgccgctcttcttttgtgcttctttactctctctcttccacagttagctaatctctttcctactaatttgtttctgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA