Sequence
atgc intronic sequence ATGC exonic sequencegtcagtaataaaattgaattttcttttaatgaaacagttgattctttagttatatagttttgaatctcatgaaaatgttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46710.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
------gtcagtaataaaattgaattttcttttaatgaaacagttgattctttagttatatagttttgaatctcatgaaaatgttttgatgt----tgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
| | | | | || || | | || || | ||| | || | | || | | ||||| ||| || ||||||| || ||||| |||||| | || || ||||||||||||||||||||||||||||| ||||| | | || ||| |||||| || || || |
tttcttcctaccagtgaggcccgtataactgtttgt-atgcacatgttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
upper sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
----gtca-gtaataaaattgaattttcttttaatgaaacagttg-attctttagttata-tagttttgaatctcatgaaaatgttttgatgttgt--agATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
||| | | || || || || | ||| | || | ||| |||| |||| | | ||| | ||| | | ||||||| || ||||| |||||| | || || ||||||||||| |||||||| |||||||| ||||| | | || ||| |||||| || | || |
ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
upper sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------gtcagt--aataaaattga--attttcttttaatgaaacagttgattctttagttatat---agttttgaatctcatgaaaatgttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG-
| || | |||| ||| | ||||| |||| | || | ||| | | || | | | | | | | | || || ||||||| || ||||| ||||| || || |||||||| |||||||||||||| || ||||| ||||| || | | | ||||| || || | || ||
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatat-ctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGC-GATAT
upper sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ22564 (Selaginella moellendorffii), 3'ss of exon 4
gtcagtaataaaattgaattttcttttaatgaaacagttgattctttagttatatagttttgaatctcatgaaaatgttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
| || ||| || ||| || || ||| | | | | ||| | | ||||| ||| ||||||| ||||| |||| |||||||| ||||| || |||||||||||| |||| ||||| |||| | | || || || ||| || | || |
-------------gtacgttcctctttcatttggtgcttggttttt--gttttcttttctgtaatgtattt----ccttttgctgtcccagATGGCGGATCCACTAACAGCACTCATGCACGCTGTACAAGTGATGAACATTCTAAAGACGCTGATTGTGAGGACACTACGGGACAGGCAAGAGGCTGTG-
upper sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ12967 (Selaginella moellendorffii), 3'ss of exon 4
gtcagtaataaaattgaattttcttttaatgaaacagttgattctttagttatatagttttgaatctcatgaaaatg-ttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
| | ||| | | || ||| ||||| || | | | || | | ||| | | ||||| ||| ||||||| ||||| |||| |||||||| ||||| || |||||||||||| |||| ||||| |||| | | || || || ||| || | || |
---------------gtacgttcctcttt-----catttggttcttggtttttgttttgttttctgtaatgtatttccttttgctgtcccagATGGCGGATCCACTAACAGCACTCATGCACGCTGTACAAGTGATGAACATTCTAAAGACGCTGATTGTGAGGACGCTACGGGACAGGCAAGAGGCTGTG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgattctttagttatatagttttgaatctcatgaaaatgttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
ttttgat putative branch site (score: 4)
tttagttatatagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtaataaaattgaattttcttttaatgaaacagttgattctttagttatatagttttgaatctcatgaaaatgttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA