Sequence
atgc intronic sequence ATGC exonic sequence...caggaaattttgcagagtaatatatactttttgtgataataaaatttgcagtaacaaaattcagtcaaaacttaacacaactcttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61910.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
-caggaaattttgcagagtaatatatactttttgtgataataaaatttgcagtaacaaaattcagtcaaaacttaacacaactcttgttttttc-tatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
| | |||| ||| | | || | || || | ||| | ||| || |||| | | | | | | |||| ||||| ||| | |||||| | |||||||||||| |||||||| | ||||| |||||||||||||| || || ||||| || || ||| | || || |
gtacgtaattaagcacacacacatcgatcaatt----cgatcgatttt----tgacatgttttgatcaatgtggcatgtgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC
upper sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
caggaaattttgcagagtaatatatactttttgtgataataaaatttg--cagtaacaaaattcagtcaaaacttaacacaactc-ttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
||||| || |||| ||||| | || | | | | || || | || || | | || ||||||||| || || |||| | || ||||||||||||||||| | ||||| |||||||||||||| ||||| || | | |||||| | |||| ||
--------------------------------gtgatgattttttttgctcagtagctaagat-aattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
upper sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
caggaaattttgcagagtaatatatactttttgtgataataaaatttgca--gtaacaaaattcagtcaaaacttaacacaact--cttgttttttctat-gtagAGATGTGTAAGATT----GGAACGACGCCG-----CAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
| || | || | | | | | || | || | || |||| || || | | | || || || | || || | |||| | || |||||| | || | ||| || ||| | |||||||| | ||||||||||||||||||||| |||||||| | | ||||| |
--gcaagatcatcacactcaagtgc-caacctgaagcacgtgcatgtacattgtaatccaaggaag--agtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
caggaaattttgcagagtaatatatactttttgtgataataaaatttgcagtaacaaaattcagtcaaaacttaacacaactcttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
||| | || || | | || | | | | | | || | || | || || | | | ||||| ||||||||| ||| | | |||| ||| |||||||||| || || |||||||||||||||||||| || ||| | ||||||||||||||| |
----------------gtagtctagtctcctcc---------atttcgatatgattgcacaccactgacacctctttca-ttgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
caggaaattttgcagagtaatatatactttttgtgataataaaatttgcagtaacaaaattcagtcaaaacttaacacaactcttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
||| | || || | | || | | | | | | | || | || | || || | | | ||||| ||||||||| ||| | | |||| ||| |||||||||| || || |||||||||||||||||||| || ||| | ||||||||||||||| |
----------------gtagtctagtctcctcc---------atttcgacatgattacacaccactgacacctctttca-ttgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcagtaacaaaattcagtcaaaacttaacacaactcttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
ctcttgttttttctat CT-rich tract
taacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caggaaattttgcagagtaatatatactttttgtgataataaaatttgcagtaacaaaattcagtcaaaacttaacacaactcttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
caggaaa
- - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaca