Sequence
atgc intronic sequence ATGC exonic sequencegtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 3
--------------------gtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
|| ||| | | | | | || ||||| ||| | | | ||| ||| | | ||| |||| || ||||||| || ||||| || ||||| || ||| | || ||||||||||| |||||||||||||| || ||||| || || ||||| || ||||
ttttcttattgaacaagtcaactggaggtttctggattatctgtgtaacctagttccag--aatttgagcagaattttcaag--taacgatctctgtactgcagGTTGAACTGGAGGATCCTGTTGAAAATATTGGAGCTAAGTTGGTTAGGCAAGCAGCAGCAAAGACCAATGATTTAGCTGGAGATGGCACAACTACTTCTG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 2
-gtatgaaatttattgtctgtttaa----ccaattatgttcctttcg-------tttttaattacttctct--aagcttaa--ggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
|| |||| || || | || || || || || || ||||| | || | | | |||| | ||| | || |||| ||||||||||| ||||||||||| ||||| || ||| | || || ||||||||||| ||||| || |||||||||||||| || || || || || |
tgtttgaatttgtttatgtggataggatttcatttgaattttgtttaagtgggttttttgggtgtttgttttgatgctttgttgaatttgatttgggaagGTTGAGTTGGAGGATCCGGTTGAGAATATTGGCGCCAAGTTGGTGAGACAAGCAGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACTTCGG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 2
-----------------gtatgaaatttattgtctgtt-taaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
| || |||| | | || | || | || || |||| | || | | | | ||| | || | |||| ||||||||||| || |||||||| |||||||| ||| | || || ||||| ||||| ||||| || |||||||||||||| || || || || || |
tttgaatttgtttacgtggataggatttcatttgaattgtgtttaagtggattgttt--gtttgtgtttgtattgatgttttgttgaatttggtttggtaagGTTGAGTTGGAGGATCCCGTTGAGAATATTGGTGCCAAGTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
| | || | | || | | ||| | | |||| | | | || ||| || || ||||| ||||||||||| || |||||||| |||||||| || | || || ||||||||||| |||||||| ||||||||||| || || |||||||||||||
atgcctaccatctgtccttgacgttgagattgtctccagtaaatatctcaacacaaatttgtccgtgaggcacttattgatgtttt--gttatcaccta--tagGTTGAGTTGGAGGATCCTGTTGAGAATATTGGTGCTAAATTAGTGAGACAAGCAGCTGCCAAGACCAACGACTTGGCTGGGGATGGGACAACAACATCTG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------gtatgaaattt-attgtctgtttaaccaattatgt-tcctttcg---tttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
| || | ||| || | | || || | | | | || | |||| ||||| | || | | | | |||| ||| | ||||| || || |||||||| ||||| ||| | || |||||||| || || ||||| ||||||||||||||||||||||| || || ||||
gttagggcttgcatcctctctatgagcccggatttattatgttgtttacttggtttttttggataagcgcgattttttttttgaggggggcggggtgtagaatcttgggataaggtttcgttctttcttgaattagatgcgcatgagtttgagcttttcaattaacgcgctgaatctcggaactca------acagGTTGAGCTTGAGGATCCAGTCGAGAACATCGGTGCCAAGTTGGTGAGGCAAGCGGCAGCCAAGACGAATGACTTGGCTGGTGACGGTACCACCACCTCTG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgctt-agGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
||||| |||| ||| | || | || | | | | | | || || | || ||||| |||||||||||||||||||||| || || || |||||||| ||| | || ||||| || |||||||| || || || || || ||
----------------------------gtatgtgccttgtctttcttgttgatgctgtggtttgctgatggaaatgtattttagATTGAATTGGAAGACCCGGTTGAGAACATTGGTGTGAAACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGAACGACGACTTCCT
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16507 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgctt-agGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
||||| ||| ||| | || | || | | | | | | || || | || ||||| |||||||||||||||||||||| || || || |||||||| ||| | || ||||| || |||||||| || || || || || ||
----------------------------gtatgtgtcttgtctttcttgttgatgctgtggtttgctgatggaaatgtattttagATTGAATTGGAAGACCCGGTTGAGAACATTGGTGTGAAACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGGACGACGACTTCCT
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
|| | | | | | || | || | | | | | || | | || | ||| |||| ||| |||| || | || |||||||||||||| ||||||||| ||||| || |||| || ||||||||||||||||| || || || || || |
------------------gtaggaaggaaaagataaaatgcggctacaa--agtcttttgtgtttttgctctttgtttgc--agGTGGAGCTGGAAGATGCAGTCGAGAACATTGGTGCGCGGCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGMapped 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|125135678|gb|EL175868.1|EL175868EST: TATGGATCCCCAAGAATTGTTTAATTGATGGTGTCACTGTTGCGAGGGAG GTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGG
genomic: TATGGATCCCCAAGAATTG-TTAA-TGATGGTGTCACTGTTGCGAGGGAGgtatgaaatt ... ttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
ttttaat putative branch site (score: 3)
ttttcttctgctt putative PPT
tttcgtttttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaaatttattgtctgtttaaccaattatgttcctttcgtttttaattacttctctaagcttaaggttttcttctgcttagGTCGAGTTGGAGGACCCGGTTGAGAACATTGGTGCAAAGCTTGTAAGGCAAGCAGCTGCAAAGACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG