Sequence
atgc intronic sequence ATGC exonic sequenceTGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagttgaaagaaagttttcaacttaagtaaaggtactggaggattttcttacaaactggttatttccctatctcattag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12170.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagt---tgaaagaaagt-tttcaacttaagtaaaggtactggag-gattttcttacaaactggttatttccctatctcattag
|| |||||||| ||||||||| |||| |||||||| || ||||| || |||| |||||||||||| | |||||| | |||||| |||||||| ||| | | | | || | ||| | | | | || || || ||| || || || ||||
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacctcatttatagcactccaattctacctttcagattcaagcaatatttttatgaatc--ttcctttttcatctag----
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G088440_T01 (Zea mays), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagt---tgaaagaaagt-tttcaacttaagtaaaggtactggag-gattttcttacaaactggttatttccctatctcattag
| |||||||| ||||||| |||||| |||||||| || ||||| || |||| |||||||||||| | |||||| | |||||| |||||||| ||| | | | | || | || | | ||| || || || ||| || || ||| ||||
AACCAAAGAGAAGTTTCAGCTGTTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgcgcacctcatttatagcactctaattctacctttcagactcaagcaatatttttatgaatc--ttcttttttcatctag----
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G129987_T01 (Zea mays), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaag----ttgaaagaaagttttcaacttaagtaaaggtactggaggattttcttacaaactggttatttccctatctcattag
|| |||||||| ||||||||| |||| |||||||| || ||||| || |||| |||||||||||| | |||||| | |||||| |||||||| ||| | | | | | || | | | | || | | | || | || | || | || || ||||
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATGATgtgggcacctcatttgtagcactccagttctacctttaagattcaagcaatatttttc----tgaatcttcctttacatc-ttag
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G090689_T01 (Zea mays), 5'ss of exon 1
--TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTC-TATGATCAAACTGGCTCAGTTGATGATGC-Tgtaagttgaaagaaagttttcaacttaagtaaaggtactggaggattttcttacaaactggttatttccctatctcattag
||||||||||| ||||||| | |||| |||||||| || ||||| || |||| |||||||||||| | |||||| | |||||| |||||||| | | || | | ||| | | | | || ||| | ||| || || || ||||
GAAGCTAAAGAGAAGTTTCAGCTGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCGTTTATATGATGATACTGGCATCACTGATGATgtgcgcaccttatttatagcactccaattctacctttcagattcaagcattattttatgaatc--ttcctttttcatctag----
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G885923_T01 (Zea mays), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagt---tgaaagaaagt-tttcaacttaagtaaaggtactggag-gattttcttacaaactggttatttccctatctcattag
|| |||||||| ||||||||| |||| |||||||| || ||||| | |||| |||||||||||| | || ||| |||||| |||||||| ||| | | | | || | ||| | | ||| || || || ||| || || || ||||
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTCGAGATGCAGAGAAAAGAGCTTTATAGGATATGACTGGCATCACTGATGATGATgtgcgcacctcatttatagcactccaattctacctttcagactcaagcaatatttttatgaatc--ttcctttttcatctag----
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G32480.1 (Glycine max), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagttgaaagaaagttttcaacttaagtaaaggtactgg-----aggattttctt--acaaactggttatttccctatctcattag--------------
||||| |||||||| ||||| ||||||| || || ||||||||||| ||||||||||| |||| |||||||||| ||||| | |||||||||||||| ||| | | |||| | | || | | ||| ||| ||| || | ||| | | | || ||| | | ||
AGCTAAGGAGAAATTCCAGCAACTGCAAAAAGTGATATCGATTCTCGGGGATGAAGAGAAGCGAGCTCTCTATGATCAGACTGGTTGTGTTGATGATGCTgtgagt-gccacttttttttttcttcatgtgttgttgctgatgattaggctttgattggataaatttctcaattag-tatttaactatttataggaaaagaa
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G12350.2 (Glycine max), 5'ss of exon 2
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagt-tgaaagaaagttttcaacttaagtaaag-gtactggaggattttcttacaaactggttatttccctatctcattag------------------
||||||| || |||||||| |||||||| |||||| | ||||| || |||||||| ||| | || || |||||||| ||||| | |||||||||||||||||| | | || | || || | | || | | || | | | | | |||| | | ||| ||||
AGCTAAAGCAAAGTTTCAGCAATTGCAAAACGTTATTGCTATTCTTGGGGATGAAGAAAAACGGGCCGTTTATGATCAGACTGGTTTTGTTGATGATGCTgtaagtgtttctgtaaagtcataatatacttgatttataatttacaatgtctggatacatggcttatctttatgtct-attaactcacattggagtcagga
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G31080.1 (Glycine max), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagt-tgaaagaaagttttcaacttaagtaaag-gtactggaggattttcttacaaactggttatttccctatctcattag------------------
||||||| || |||||||| |||||||| ||||| | ||||| || |||||||| ||| | || || |||||||| ||||| | |||||||||||||||||| | ||| || | || | | ||| | | || | | | | | |||| | | ||| ||||
AGCTAAAGCAAAGTTTCAGCAATTGCAAAACGTTATCGCTATTCTTGGGGATGAAGAAAAACGGGCTGTTTATGATCAGACTGGTTGTGTTGATGATGCTgtaagtgtttaagtaaagccatattatacttgatttgtaatttacaatgtctggatacatggtttatctttatgtct-attaactcacattggagtcagga
upper sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 5'ss of exon 3
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagttgaaagaaa--------gttttcaa----cttaagtaaaggtactggagga--------ttttcttacaaactggttatttccctatctcattag-----------------------------------
|| || || ||||||||||| | |||||||| || || ||||| ||||||||||||||||| ||| |||||||||| ||||| | |||||||||||||||||| | | || ||||| | ||| ||| || | | |||| | | | || || || | || || | ||| |
AGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATGCTgtaagtgaatatgaaaaccttttgttttgtatgttcttttttaatggcatttgagggcacaaatgtgtccataagaattgatgatatctattgatcaggaagtgtgcatcttatttctcaatttttttatgatcagMapped 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|125035309|gb|EL107578.1|EL107578EST: CTATGATCAAACTGGCTCAGTTGATGATGCT GATCTTTCGGGAGATGTGGTTGACAACTTGAGGGACTTCTTCAAGGCAATG
genomic: CTATGATCAAACTGGCTCAGTTGATGATGCTgtaagttgaa ... atctcattagGATCTTTCGGGAGATGTGGTTGACAACTTGAGGGACTTCTTCAAGGCAATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagttgaaagaaagttttcaacttaagtaaaggtactggaggattttcttacaaactggttatttccctatctcattag
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG