Sequence
atgc intronic sequence ATGC exonic sequence...atctgtttattgtatatttattgcatggtttcagtttatttcgtgaagcaatacaactgatgaatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20800.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 3'ss of exon 6
atctgtttattgtatatttat-tgcatggtttcagtttatttcgtgaagcaatacaactgatgaattt-gttgttatgccttttcttcgttc-ttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
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---tcttcataagaaaataacacactaaagaaccttttagctcttgtttttgtttctgtgaaaaattccatttccctctctcattttcttttgttcttttcagCTCATATTCCCCTGTACCTGTACCCATTCTTGAATACTACCAGCAAGACAAGACCTTTTGAATACCTGCGACTCACCAGCCTGGGTGTCATCGGTGCACT
upper sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G10400.1 (Glycine max), 3'ss of exon 4
--atctgtttattgtatatttattgcatggtttcagtttatttcgtgaagcaat--acaactgatg-aatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
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tcacaagatccat-tccagtttttgcttg-ttaaaggatagtacatgaagtgtttgatatttcatacaataaattgttgcacttgctttttctcctt---tgcagCTCATATACCTCTATATCTGTATCCCTTCCTTAATACAACAAGCAAGTCAAGACCATTTGAGTACTTGAGGCTTACCAGCCTTGGTGTCATTGGTGCATT
upper sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G43220.1 (Glycine max), 3'ss of exon 4
atctgtttattgtatatttattgcatggtttcagtttatttcgtgaagcaat--acaactgatg-aatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
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cacaatatccgttatggtttttgctcgttaaaaggaccttacacgaagtgtttgatatttcatacaatgaattgttgcacatgctttttctcctc---tgcagCTCATATACCTTTATATCTGTATCCCTTCCTTAATACAACAAGCAAGTCAAGACCATTTGAGTACTTGAGGCTTACCAGTCTTGGTGTAATTGGTGCATT
upper sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G02480.1 (Glycine max), 3'ss of exon 4
--atctgtttattgtatatttattgcatggtttcagtttatttcgtgaagcaataca-actgatgaatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
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atatccgttt-cagcagggtttttgc-tcattgaaattaacacttaaaggaaaaagatattactctgttcactctt-tacacttacctttttctcatctgcagCTCATATACCTCTATATCTGTATCCCTTCCTTAATACAACCAGTAAGTCCAGACCATTTGAGTATTTGAGGCTTACCAGTCTTGGAGTCATTGGTGCCTT
upper sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G46250.1 (Glycine max), 3'ss of exon 4
--atctgtttattgtatatttattgcatggtttcagtttat-ttcgtgaagcaatacaactgatgaatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
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atatctgttt-cagcagggtttttgc-tcattgaaattaacacttgaagggaaaagatattactatgttcactctt-tacacttacctttttctcatctgcagCTCATATACCTCTATATCTGTATCCCTTCCTTAATACAACCAGTAAGTCCAGACCATTTGAGTATTTGAGGCTTACCACTCTTGGAGTCATTGGTGCCTTMapped 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|124781191|gb|EH871134.1|EH871134EST: AATGTTATTTCTCAAGG CTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCA
genomic: AATGTTATTTCTCAAGGgtaatgttct ... ttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCA
EST:
gi|124869758|gb|EH954195.1|EH954195EST: TGCGTAGCATCTCATTCTGACACGAGAATGTTATTTCTCAAGG CTCATATCCCGTTGTACCTTTATCCC
genomic: TGCGTAGCATCTCATTCTGACACGAGAATGTTATTTCTCAAGGgtaatgttct ... ttgtgcacagCTCATATCCCGTTGTACCTTTATCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcaatacaactgatgaatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
aactgat putative branch site (score: 3)
ttatgccttttcttcg putative PPT
atgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctgtttattgtatatttattgcatggtttcagtttatttcgtgaagcaatacaactgatgaatttgttgttatgccttttcttcgttcttgtgcacagCTCATATCCCGTTGTACCTTTATCCCTTCCTTAATACAACGAGTAAGTCCAGACCTTTCGAATACTTGCGGCTTACTAGCCTAGGTGTCATCGGTGCACT
- - - - - - - - - - - - - - - - - - - - - - - - caataca