Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatctctctgaatgtaccatataaaatgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68060.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
gtaaaatctctctgaatgtaccatataaaatgttgttaaaaagac--gtgtttgtaatggaagtcttgata------tttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
|| | || | | | | || ||| |||| ||| || | | ||| || | || || ||||||| ||||||||||| || || ||||| ||||| |||||||| || || || |||||||| | || || ||||| |||||||| || |||||||| |
---gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
---------------gtaaaatctctctgaatgtaccatataaaatgttgttaaaaagacgt-gtttgtaatggaagtct----tgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
| | | | | || || || | | | || || | || | || | | || | || | ||| ||||||||||||| ||||| || || || || || || ||||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
---------------gtaaaatctctctgaatgtaccatataaaatgttgt-taaaaagacgtgtttgtaatggaagtct----tgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
| | | | | || || || | | | || | || ||| || | | || | || | | ||| ||||||||||||| ||||| || || || || || || ||||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
-------gtaaaatctctctgaatgtaccatataaaat----gttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
| | | || || | || | | ||| ||| | | | |||| | | || | || ||| ||||| | ||||| || || || || || || || || ||||||||||| ||||||||||||||||| ||||| ||| | |||||||| ||||| |||||||
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
-------gtaaaatctctctgaatgtaccatataaaat----gttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
| | | | | || || | || | | ||| ||| | | | ||| | | || | || ||| ||||| | ||||| || || || || || || || || ||||||||||| ||||||||||||||||| ||||| ||| | |||||||| ||||| ||||| |
gttagtatttatttgtttttggatattaatcttagatttctaattgataattataatcttagctaactgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
---gtaaaatctctctgaatgtaccatataaaatgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
| | | || || | | ||| | || | | | || | ||| | | || || | || ||||| |||| || ||||| || || ||||| ||||||||||||||||| || |||||||||||||||||||| ||||| |||||||| ||||| ||||| |
gttggtattcttgtcctcatctgtcttatgatgctttaattcatatttttgctc---atgtatttggatgtaattctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaatctctctgaatgtaccatataaa-atgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
|||| || || | ||| | | | | | | |||| | || ||||| | | || ||||| || || | || |||||||||||||| || || ||||||||| | ||||| || || ||||||||||| ||||| || || |
----------------------gtatatgcgtgggtttggctctaggtgctcatgacag-----tcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGAMapped 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|164102969|gb|ES170744.1|ES170744EST: ATCAAAGCCTCAAAGACAAGGATGATGCCATAGAG ATGTTAGCAAAAAAGGTTAGAAACTTTAACAAAGGCAATAGGAAGTTGAAG
genomic: ATCAAAGCCTCAAAGACAAGGATGATGCCATAGAGgtaaaatctc ... tttcttgtagATGTTAGCAAAAAAGGTT-GAAACTTTAACAAAGGCAAT-GGAAGTTGAAG
EST:
gi|164113228|gb|ES038294.1|ES038294EST: CTTCGTATG-AAAGGATCAAAGCCTCAAAGACAAGGATGATGCCATAGAG ATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGC
genomic: CTTCGCATGAAAAGGATCAAAGCCTCAAAGACAAGGATGATGCCATAGAGgtaaaatctc ... tttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGC
EST:
gi|125154132|gb|EL184901.1|EL184901EST: CTTCGCATGAAAAGGATCAAAGCCTCAAAGACAAGGATGATGCCATAGAG ATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAG
genomic: CTTCGCATGAAAAGGATCAAAGCCTCAAAGACAAGGATGATGCCATAGAGgtaaaatctc ... tttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
tcttgat putative branch site (score: 4)
tatttttctt CT-rich tract
ttgatatttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatctctctgaatgtaccatataaaatgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC