Sequence
atgc intronic sequence ATGC exonic sequenceGGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01090.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 2
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
|| | |||||||| || |||||| |||||| || || ||||| || ||||||||||||||||| || || ||||||| |||||||||||| ||||||||| || || | | | || || || ||| | | || | ||| ||| ||| | | | | || ||| || ||
GGCAAAGTGAAGATCGCGGAGCATATATTGACTGGTCACAAGGTGGCAATCAAGATCCTCAATCGCCGTAAGATCAAGAGCATGGAGATGGAAGAGAAAGgtt--ggtactgatccctttgacccttttgttcaagatgt--ttgtagaatatatacgaaatg-atagatacttgggtaaatatttaagatccatcacatgtttc-------------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 2
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
|| | |||||||| || |||||| | ||||| || | |||||||| |||||||| || |||||| |||| | || ||||| ||||||||||||||||| || | | | ||| | | | | | | | | || || || | |||| || | ||||| | | || || | ||||||
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGGCACAGAGTTGCTATAAAGATCCTGAACCGTCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaccttccttttataaagagaccactttaatcaatctattatctt-ctgtgttcatg-atcatatgt-tacct-gcttcctata-gtggtctgatatgtgaact-------------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 3
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
|| | |||||| || || || |||| ||||| || ||||||||||| ||||||||||| || || ||||| || ||||||||||| ||||| || |||||| | ||| | |||| | || ||| || || | | || | || || ||||| | | | || |||| || || || | | | |
GGCAAGGTGAAAATTGCAGAACATGTGTTGACTGGCCATAAGGTTGCGATCAAGATCCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatgttgttttttataaataaatttcaatcctttttttaattttagatattcc---aatattt---cctgcaattttgtttt-gttttgttttgtgaatattga-----------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 2
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
|| | ||| || || || || |||| |||||| || ||||||||||| |||||||| || || || ||||| || ||||||||||| ||||| || |||||| | || | |||| | || ||| || |||| | | | || || | | | ||||| | ||| || | | ||||| | | || ||| || ||
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattgttttttataaataaatttca-----attgtcatctaattgtggtcct----tttttaaattt-tagattttccaatat-ttcctgc-----agtttgttttgtttt--------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 2
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagtt--ttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
|||| ||| || || || || |||||||| || ||||| || ||||||||||||||||| || ||||| || || ||||||||||| ||||| || ||||||| | ||| || | || | | | || | || || | | ||| || | | | ||| || || | | || | |
GGTAAGGTTAAAATTGCAGAACATGCATTAACTGGACACAAAGTTGCTATCAAGATCCTTAACCGTCGGAAGATAAAGAACATGGAAATGGAAGAAAAAGgtatggttcacttgcttggatgatgaccttgtctgtcccagtaagttaacaatcgtattgtgtcattt---tgtgtagattgttatgattgttaaattgtcac-----------------------
upper sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EDO99409 (Chlamydomonas reinhardtii), 5'ss of exon 2
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
|| ||| | || ||||||| | || || || ||||| || || ||||||||||| || || |||||| || | ||||||||||||||||||||| | | |||| || || | | | | | |||| || | | | | || | | || | |
------GTCAAGGTCGCGGAGCATGTGCTCACGGGGCACAAGGTGGCGATTAAGATCCTCAACCGGCGTAAAATCCAGCAGATGGAGATGGAGGAGAAAGgtg--gggcgcg---tgtgaatggggcggggtgaaggagcggggtacgtgcggtgttggggcgggtacgtgtg-gccggcggcgctgtgacgccagccgtggccgt------------------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|125227005|gb|EL241090.1|EL241090EST: AGATGGAGGAGAAAG TGAGGAGAGAGATCAAAATCTTGAGACTATTTATGCATCCTCACATCATCC
genomic: AGATGGAGGAGAAAGgtacaagttt ... tttgatgcagTGAGGAGAGAGATCAAAATCTTGAGACTATTTATGCATCCTCACATCATCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA