Sequence
atgc intronic sequence ATGC exonic sequenceAGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagccgccttctaacatctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52360.2 |
intron # | 24 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 24
-----AGGCTGACGAAGAGTGGGGTACG-AATAATGAAGGAAACCCATCAGCCTAATAGCAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagccgccttctaacatctttttccgttgatgtgtg--tctggtttcaagtcattgcatttcatagcaacccttaggaac
|| | |||| | | | | | | | ||| | || | || | || | || ||| | | | | | || || | ||||| | |||| | || | || | || |||| || || | | || || | || | |
AATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGGTAACGAGGCTGACGAAGAGTGGGgtacgaataatgaa---ggagccccgtca----gcctaaaagcaattggttggggtggtgtgaaaatcgaaattttgtctctggtgattaattgt--ttctgaag---
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 24
----------------------------------------------------------------------------------AGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagccgccttctaacatctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac
||||||||||||||||||||||||||||||||||| ||| ||||||||| ||||| | ||| || ||| ||| | ||||||||||||||||||||||||| | | ||| |||
AATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGGTAACGAGGCTGACGAAGAGTGGGgtacgaataatgaaggagccccgtcagcctaaaagcaa-ttggttggggt-ggtgtgaaaa----tcaaaattttgtctctggtgattaattg---tttctgaagtgcc-------------------------------------------------------------------------
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 24
----------------------------------------------------------------------------------AGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagccgccttctaacatctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac
||||||||||||||||||||||||||||||||||| ||| ||||||||| ||||| | ||| || ||| ||| | ||||||||||||||||||||||||| | | ||| |||
AATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGGTAACGAGGCTGACGAAGAGTGGGgtacgaataatgaaggagccccgtcagcctaaaagcaa-ttggttggggt-ggtgtgaaaa----tcaaaattttgtctctggtgattaattg---tttctgaagtgcc-------------------------------------------------------------------------
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
-AGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGT-CGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagc-cgccttctaac--atctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac
| | || || || || |||| || |||| || | ||| | || | || || | | | || | | || |||| | | ||| | | || | | | | | || | | | ||||| || | ||| | | |
TACACAGAGGAGCAGGAGGAACAGAATGGAGA-GGAAGGAAGCCAAGAGGA-GGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg---
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 25
----------------------------------------AGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattcccc-gaaaagccgccttctaacatctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac
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GCTGATTCTACTGATGGTGCAGTACTCGTTAATGGTAACGAGGCTGAAGAAGAGTGGGGTACGAATAATGAAGGAACTCCATCGGCCTAAAAGGCAATTGgttg-ggccagtgt-gaaaatcc---aaattttgtctctggtgattaattgattttctttgaagtgccatctctgactcgcagtttgagtttttgt---ccttgctac---------------------------------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|125036120|gb|EL108389.1|EL108389EST: CAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTG TGCTTACACCGCGTCAGTAGAGTTTACAGTTTATGGGAATGGTGAAAGTTC
genomic: CAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatt ... ttttttgcagTGCTTACACCGCGTCAGTAGAGTTTACAGTTTATGGGAATGGTGAAAGTTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGTCGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagccgccttctaacatctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG