Sequence
atgc intronic sequence ATGC exonic sequenceATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01320.2 |
intron # | 19 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: LOC_Os07g23990.2 (Oryza sativa), 5'ss of exon 17
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtt----tagcactcttgattttaaaagaatcgcgaggtta-----gatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttag
|||||||||||||||| || ||||| || |||||||||||||||||||| ||||||||||| ||||| || | | || |||||||| |||||||| ||||||||| | | || || | ||| || | | | ||| | || | | ||| | || |
ATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCTACTACCGTTTACAACATACAGAACTGGCTCTAAAgtaagttgactttatgtttttttttccctgaagatcatctatctatccataagaatgaacatgactatagttcccctttgaggtcttagttgaagtaata-------------
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA16G02770.1 (Glycine max), 5'ss of exon 19
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggata-tgattgttt--ttgttag
| |||||||| | || || |||||||| ||||| |||||||| ||||| ||||||||||| |||||||| || ||||| || |||||||||||||| ||||| |||| || || || || | | | | | | | || | | ||| | || | || | | | || ||| | ||| || ||||||
ACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCTATTACAGACTTCAACACACAGAGCTGGCTCTGAAgtatgttttgctcttgtg----caatatagtgatgta-taatttttcttgagtttttaaagtttaatttggtt-tttgaattaatataatacttgcttaattgtta-
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA07G06160.1 (Glycine max), 5'ss of exon 19
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattttaaaagaatcgcgaggttagatgg--tttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttag
| ||||| || | || || |||||||| ||||| |||||||| ||||| ||||||||||| |||||||| || ||||| || || ||||||||||| ||||| |||| || || || | | || | || ||| ||| || |||| || | ||| | | ||| | | || || ||||
ACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCTATTACAGACTTCAACACACCGAGCTGGCTCTGAAgtatgttttgctcttgtgcaatatagtgatgtctaacttttcatgagtttttaaagtttaatttagtttt---tgaattaatacaatacttgcttaattttta---
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 5'ss of exon 4
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattt-taaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttcc-atcatctaaacctggatatgattgtttttgttag
||||||| ||||| ||||||||||||||||| || |||||||||||||| ||||||||||| |||||||| | ||||| || || || |||||||||||||| ||| | | || | || | | || || |||| |||| | |||| | || | | | | | || | |||
ATGAGAGAGAACTAGGACTTGATCATCCAGACACGATGAAGAGTTATGGAGATCTTGCTGTGTTCTATTACGGACTTCAACACACTGAACTGGCTCTCAAgtatgttggtcttgtgtaatgcactattgacttttcatgtattatt-cataaacatttgtgctttcttgcttgaaatttcagcagtcaagttatattgttt-----
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 5'ss of exon 19
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattt-taaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttcc-atcatctaaacctggatatgattgtttttgttag
||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||| || ||||| || ||||| |||||||||||||| ||| | | || | ||| | | || || |||| |||| | |||| | || | | | | | || | |||
ATGAGAGAGAACTAGGACTTGATCATCCAGACACAATGAAGAGTTATGGAGATCTTGCTGTGTTCTATTACAGACTTCAACACACAGAACTGGCTCTCAAgtatgttggtcttgtgtaatgcactatagacttttcatgtattatt-cataaacatttgtgctttcttgcttgaaatttcagcagtcaagttatattgttt-----
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 5'ss of exon 13
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtt-tagcactc---------ttgattttaaaagaatcgc--gaggttagatggttt---aaatgtttgatgtct---ctttccatcatctaaacctggatatgattgtttttgttag-----------------------------
||||| | |||||||||||||| || |||||||| ||||| |||||||||||||| || || || || ||| | ||||| || || ||| |||| || ||||||||| || || | || |||| ||||| | || | ||| || | | || || ||| | |||| | | ||| | || | | |
ATGAGCGAGAACTTGGACTTGACCACCCAGATACCATGAAAAGTTATGGTGATCTGGCAGTATTTTACTATCGTCTTCAACACACCGAGTTGGCACTTAAgtaagttctaatacccaagcacaggtttctttttggagaatggtctaagatcagagtgtctttgagatcgttaatgattagttgttccgatttttgaactggaattatacgggaaggactgccgctcaatttttattttgttggaatgcag
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: PP1S363_15V6.1 (Physcomitrella patens), 5'ss of exon 14
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagttt----agcactcttga---ttttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcat-ctaaacctggatatgattgtttttgttag------------------------
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ATGAGCGAGAGCTTGGTCTAGATCATCCAGATACCATGAAGAGTTATGGGGATCTGGCAGTATTTTATTATCGCCTTCAACATACGGAATTGGCACTGAAgtaagtcctggaaacaaagttaaagtttctgaaatcgttcagtgttgataagattgttctgcgtagtgccgcaatgagtcaagttgaaacagtgtgcaagtattgccgctcaatttttgttgttgttgggatgcag
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttag
|||||||||| ||||||||||| ||||| ||||||||||| || |||||||| | |||||||| || || |||||||| ||||||||| |||| | | |||| || || || || | | | | | | || |||
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagtt-gctcttttaagtagtgtactctattaacttctga-ggtcag------------------------------------------------------Mapped 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|116396583|gb|EG439175.1|EG439175EST: GATCTTGCTGTCTTCTATTATAGACTTCAGCATACAGAGCTGGCTCTCAA GTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCA
genomic: GATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttag ... tttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT