Sequence
atgc intronic sequence ATGC exonic sequenceTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 2
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattc-tttactactgcattttatctcttgttgcctgctatgtcctatgaat--
| || || || ||||||| |||||||| ||||||||||| || ||||||||| || || |||||||| | | || || || | ||| |||| | || ||| || | |||| | ||| | | | ||| |||| | || | |||| |||| ||| | | | || | | | | |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgatta-tcggtttgtttcaaaatatat--attgactttttcttttctaatttatctctgcttttagacccattttctattttgttgaagacaggtta
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat---
| || || || ||||||| |||||||| ||||||||||| || ||||||||| || || |||||||| | | || ||||| | ||| |||| | || ||| || | | |||| || ||| | | | ||| |||| | || | |||| |||| ||| | | | || | | || | |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgatta-tcagtttgttccaaaatatat--attgactttttttttctaatttatctctgcttttagacccattttctattttgtggaagacaggttat
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 6
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattc-tttactactgcattttatctcttgttgcctgctatgtcctatgaat--
| || || || ||||||| |||||||| ||||||||||| || ||||||||| || || |||||||| | | || || || | ||| |||| | || ||| || | | |||| || ||| | | | ||| |||| | || | |||| |||| ||| | | | || | | || | |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgatta-tcagtttgttccaaaatatat--attgactttttcttttctaatttatctctgcttttagacccattttctattttgtggaagacaggtta
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtat--gttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat
| || | || |||||||||||||||| ||||| ||||| || |||||||| || |||||| ||||| |||| |||||||||||||||| ||||||| ||| ||||| | || || | | | | | | |||| || ||| | | || | ||| | ||| ||| | | || | |
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtagtagttattttctgttatgttgttacggaatgacccttactttc--tttatttagaaattatgtttgatatgttttgagaaaggcttttttgtaagggt
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat------
|||| | ||| ||||||| |||||||| ||||||||||| || |||||||| || |||||| ||||| |||| |||| || |||||||| ||||||| ||| | || || || || | ||| ||| ||| ||| || | || ||| | ||| | | | |||| | | |
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtaggacttaccttgttgcaagacaa--tgattg-attttctttcaat--atgtagaaata-tgcttgatatgtgtagaaattaaaaatgtttttggtaacagaat
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 6
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaatt-ttttgcattcacttataatt-cattctttacta-ctgcattt--tatctcttgttgcctgctatgtcctatgaat
| || | || |||||||||||||||| || || ||||| || |||||||| || |||||| ||||| |||| |||||||||||||| | ||||||| ||| ||| ||||||| | || || || | | || | || || |||| |||| | | ||| ||| | ||| ||| | | || |
TACTTTTAAGTTTGATTGAATACAAGACACTAGTCATGCGCGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGTATCATAACAGgta----gtag-ttattttcttttatgttattacagaatgacctttactttcattatttagaaattatgtttgatatgttttgagaaaggcttttttgtaaggga
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat--
|||| | ||| ||||||| |||||||| ||||||||||| || |||||||| || |||||| | ||| | || |||| || |||||||| ||||||| ||| | | |||| ||| || || | ||| ||| ||| || | || | | | | | | | || ||| |
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgta-gaagttagttaccttgtgttacgttgcaagataatgattaattttctttcaata-tgttgaaatatgcttgatatgtgtagaaattaaaaatgctttt
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattc-tttac--tactgcattttatctcttgttgcctgctatgtcctatgaat
| || || || ||||||| |||||||||||||||||||| || || |||| | |||||| || |||||||| ||||||| ||||| || ||||| | ||| || | || | | | | || | | || | || | |||| | | |||| | | || | | || |
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctact--gttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttcatgttttgtggggaattttgta-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|164208735|gb|ES100258.1|ES100258EST: TCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAA TGTTGCTCATTTCTTGGAATCTCGGGGAATGATTGAAGATGCTTTAGAAAT
genomic: TCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttata ... taatattcagTGTTGCTCATTTCTTGGAATCTCGGGGAATGATTGAAGATGCTTTAGAAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG