Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgactctctatctctgttaatctttcgttctttttgggttacaggcttttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04340.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
----------gtacgtgactctctatctctgttaatctttcgttctttttgggttacaggctt----ttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
| ||| | | || || || || | |||||||| | | | ||| | || | | || | ||| |||||||| || | ||| ||||| || || || |||||||||||||| ||||| |||||| ||||||||||||||||||| || || || || || ||| |
catgctcttcatttgtgctacaatttc-ctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 9
--------gtac-gtgact-ctctatctctgttaa--tctttcgtt---ctttttgggt-tacaggcttttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
|| | | | | | | | |||| |||||||| | ||||| || || || | || ||| |||| | | |||||| || | ||| ||||| || || || ||||| |||||||| ||||| ||||||| |||||||||||||||||| || || || || ||||| |
atttgaaggtcctgctattaccatggcatatttaagccctttcgtttctccttttgcgtgtatgaatttatttatattgtctatttttcctcgtt---tacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 2
------gtacgtgac---tctctatctctgttaa---tctttcgtt---ctttttgggt-tacaggcttttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
||| || || | | | | | || | |||||||| | ||||| || || || | || ||| |||| | | |||||| || | ||| ||||| || || || ||||| |||||||| ||||| ||||||| |||||||||||||||||| || || || || ||||| |
tttctggtatgtcactaatttgaaggtatatttaagccctttcgtttctccttttgcgtgtatgaatttatttatattgtctatttttcctcgtt---tacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 9
----------gtacgtgactctctatctctgttaatctttcgttctttttgggttacaggcttttctaaggactc----ttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
| | | | | | | || | | | | | | || ||||| | || | || | ||||||||| | ||| |||| |||| || ||||||| || || || ||||||||| ||||| ||||| ||||||||||||||||| ||||| || | || | |||| || |
actttatgattttggctatttacgaaccatgatgttagtgctcttgtcttaatttacaccgtgttaatatgattaagaattctttttatattcatgt-cagATATCCTATTACAATTGGCACTGCAATTCCTTTGAAAGCAAGTTTCTTCATCACTTATATAATGGTTGATGGATGGGCTGGTATAGCTGCAGAGGTTTTG
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 8
----------gtacgtgactctctatctctgttaatctttcgttctttttgggttacaggcttttctaaggactc----ttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
| | | | | | | || | | | | | | || ||||| | || | || | ||||||||| | ||| |||| || | || ||||||| || || || ||||||||| ||||| ||||| ||||||||||||||||| ||||| || | || | |||| || |
actttttaattttagctatttacgaaccatgatgttagtgctcttgtcttaatttacaccatgttaatatgattaagaattctttttatattcatgt-cagATATCCCATAACAATTGGCACTGCAATTCCTTTGAAAGCAAGTTTCTTCATCACTTATATAATGGTTGATGGATGGGCTGGTATAGCTGCAGAGGTTTTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125300181|gb|EL314266.1|EL314266EST: GGAGCTGCGTTTGAGCAGCTTAACTCTTTCCTCAATCAATCGCCTAATCA AATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAA
genomic: GGAGCTGCGTTTGAGCAGCTTAACTCTTTCCTCAATCAATCGCCTAATCAgtacgtgact ... atctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAA
EST:
gi|116432615|gb|EG475207.1|EG475207EST: GGAGCTGCGTTTGAGCAGCTTAACTCTTTCCTCAATCAATCGCCTAATCA AATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTAT
genomic: GGAGCTGCGTTTGAGCAGCTTAACTCTTTCCTCAATCAATCGCCTAATCAgtacgtgact ... atctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttttgggttacaggcttttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
tcttctttttaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgactctctatctctgttaatctttcgttctttttgggttacaggcttttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA