Sequence
atgc intronic sequence ATGC exonic sequencegtgagacacattctttgaagttctcttccttgtagcattcaagtagtgcatgtgaacctttggtgatacagattattcaaaagaaaacagagagttttttattatagctcattctttcttaatccttttctaatagtctctttttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCATTAGTGGATTGGGGAATTCCTGTTCCCGACGACGATAAGCAAACCATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55400.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G43550.1 (Glycine max), 3'ss of exon 4
gtgagacacattctttgaagttctcttccttgtagcattcaa-gtagtgcatgtgaacctttggtgatacagattattcaaaagaaaacagagagttttttattatagctcattctttcttaatccttttctaatagtctctttttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCATTAGTGGATTGGGGAATTCCTGTTCCCGACGACGATAAGCAAACCATAT
| || || | | ||||| | | || || || | | ||| | | || ||| ||| | || || | ||| | ||| |||| ||| | || |||| ||||||||||| || |||||||| || || ||||||||||| ||||||| ||| |||||||| |||||||||||||| ||| | | || || ||||
--------------------------------aggtgtttaatgaactgcatatta-tctctgttgggagaactta-----------aaatggattttcttaatgta--tcgtgctt-caaaattaacttct-----tctataaccttcaagGTTCAAAGTTGGATCAACAGTGGCTTGAGGGACTTTTCCATTTCCCGAGCATCAGTTGATTGGGGCATTCCTGTTCCCGATGACAAGACCCAGACTATAT
upper sequence: AT3G55400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G23250.1 (Glycine max), 3'ss of exon 4
gtgagacacattctttgaagttctcttccttgtagcattcaa-gtagtgcatgtgaacctttggtgatacagattattcaaaagaaaacagagagttttttattatagctcattctttcttaatccttttctaatagtctctttttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCATTAGTGGATTGGGGAATTCCTGTTCCCGACGACGATAAGCAAACCATAT
| || || | | ||||| | | | || | || | | |||| | || ||| | || | | |||| | | ||||| || || |||| ||||||||||| || |||||||| || || ||||||||||| ||||||| ||| || ||||| ||||||||||| || ||| | | || || ||||
----------------------------------gtatctaatggactgcatattatctctt-----ttgggagaacttaaaatggatttt----cttgttaatgtattgtgctttaaattaa-cttcttctacaagcttca--------agGTTCAAAGTTGGATCAAAAGTGGCTTGAGGGACTTTTCCATTTCCCGAGCATCAGTTGAGTGGGGCATTCCTGTTCCTGATGACAAGACCCAGACTATAT
upper sequence: AT3G55400.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 3'ss of exon 4
gtgagacacattctttgaagttctcttccttgtagcattcaagtagtgcatgtgaacctttggtgatacagattattcaaaagaaaacagagagttttttattatagctcattctttctt--aatccttttctaatagtctctt-tttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCATTAGTGGATTGGGGAATTCCTGTTCCCGACGACGATAAGCAAACCATAT
|||| || || | || || || | | | || || | || | | | ||||||| ||| | || | | | || | ||||| ||||||||||| || ||||| | || |||||||| ||||| ||||||| ||||||||||| ||||||||||| | ||| | ||||| |||||||
--------------------------------------------------cttgaaatttaaaagaca----ttctttaatgtattaatgtaaggttcacactaccgatgctgctttctttcaatatatcgcttctgatatagaacttctctagGTGCAAAGTTGGATCAAAAGTGGTCTGAGGGATTTTTCTATTTCCCGAGCATCTGTGGATTGGGGCATTCCTGTTCCTAATGACAACAAGCAGACCATATMapped 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|116429746|gb|EG472338.1|EG472338EST: TTTTGGCCCAGAATCCTCGTTTTGTGCAGCCTTCGTATCGTCTTAATGAG GTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCA
genomic: TTTTGGCCCAGAATCCTCGTTTTGTGCAGCCTTCGTATCGTCTTAATGAGgtgagacaca ... ttttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttattatagctcattctttcttaatccttttctaatagtctctttttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCATTAGTGGATTGGGGAATTCCTGTTCCCGACGACGATAAGCAAACCATAT
ttctaat putative branch site (score: 2)
tctctttttttgt putative PPT
ttttctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagacacattctttgaagttctcttccttgtagcattcaagtagtgcatgtgaacctttggtgatacagattattcaaaagaaaacagagagttttttattatagctcattctttcttaatccttttctaatagtctctttttttgtagGTACAAAGTTGGATAAAGAGTGGCTTAAGAGATTTTTCCATTTCTCGAGCATTAGTGGATTGGGGAATTCCTGTTCCCGACGACGATAAGCAAACCATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA