Sequence
atgc intronic sequence ATGC exonic sequencegtaatgggaattggtaatcaattttgttgagaaatttgttgagaggagactgaatttgatatcttgcttttgttgtgtagGCTGAAGGAATTTTCAGGATAAACCCTGAGAATAGTCAAGAGGAACATGTAAGAGACCAACTAAACAGAGGTATTGTACCTGAGAATATTGATGTGCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G03100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S1_829V6.2 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------------------gtaatg-ggaattggtaatcaat-tttgttgagaaatttgttgagaggagactgaatttgatatcttgcttttgttgtgtagGCTGAAGGAATTTTCAGGATAAACCCTGAGAATAGTCAAGAGGAACATGTAAGAGACCAACTAAACAGAGGTATTGTACCTGAGAATATTGATGTGCATT
|||| || | || || |||| | || || | || | || | || || | | | |||||||||| ||||| |||||||| || ||||||||||| ||||| ||||| | || ||||| |||| ||| || || |||| | || || | |||
gtgcgtccaatctgagaataacagcatgagaaatcttttatgtctgctctatttgaacattttagaacttgtctgggtcagttagcttgacctaacgtgtataacatgactgcagaatgcggtaccttccatgaacgcctgtttgcaccaagtttcaggttcaatctaactagaagttttactgt--tcattcagGCTGAAGGTATTTTTAGGATAAATCCCGAGAATAGTCACGAGGAGCATGTGCGGGAGCAACTCAACAAAGGCATCGTCCCTGCCGACATCAATATTCATG
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------------------gtaatgggaattggtaatcaattttgttgagaaatt-tgttgagaggagactgaatttgatatcttgcttttgttgtgtagGCTGAAGGAATTTTCAGGATAAACCCTGAGAATAGTCAAGAGGAACATGTAAGAGACCAACTAAACAGAGGTATTGTACCTGAGAATATTGATGTGCATT
|| | | | | | | | | || | || | | ||| | ||||| ||||| | | |||||||| || ||||||||||| || |||||||||||||| ||||| ||||| || | ||||| |||| ||| ||| ||| | | ||||| | ||
gtgtggctcacatccgaatattggctcaaatcaattttaatgccggattcctgactgtcaagcaacttaacgcacgttcagttaactggccgtttgttatcggagtgttgatcggcttatgtgtgtagcaccgtctcatgcgtgtatagttacatgatatttaaaaccaacttattttga--gcttgcactgtgcatttagGCTGAGGGTATTTTCAGGATCAATCCTGAGAATAGTCACGAGGAGCATGTGAGGGCGCAACTCAACAAAGGAGCTGTGCCTTATGACATTGACATTCACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgagaaatttgttgagaggagactgaatttgatatcttgcttttgttgtgtagGCTGAAGGAATTTTCAGGATAAACCCTGAGAATAGTCAAGAGGAACATGTAAGAGACCAACTAAACAGAGGTATTGTACCTGAGAATATTGATGTGCATT
atttgat putative branch site (score: 5)
tcttgctttt CT-rich tract
aatttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgggaattggtaatcaattttgttgagaaatttgttgagaggagactgaatttgatatcttgcttttgttgtgtagGCTGAAGGAATTTTCAGGATAAACCCTGAGAATAGTCAAGAGGAACATGTAAGAGACCAACTAAACAGAGGTATTGTACCTGAGAATATTGATGTGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA