Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaaaaacttatctgttcttggcaaattaaacaatccctaagaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G27230.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G27230.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
-----------gtaagtgaaaaacttatctgttcttggcaaattaaaca----atccctaagaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA
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gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgtttttttttctttg-atctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
upper sequence: AT2G27230.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
-------gtaagtgaaaaacttatctgt-tcttgg--caaattaaacaatccctaa-gaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA
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gtatgtagcctttcttgtgctttcctatatctcagtcctgaacatatatttcacattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
upper sequence: AT2G27230.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtgaaaaacttatctgttcttggcaaatt-----aaacaatcc-ctaagaaaggttattactaacaaagagta-catgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA
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gtaactcatctttcttcctttcttcctcacttttttgaggacattttactatattgagatactgattatgtcctctaatctactgatgtggtttaacagTGTAGCATTGATGCACTGCTTGAACGCACCATCAAGCATATGCTTTTCTTGCAAAGTGTCATGAAGCATGCAGACAAGCTAAAGCAAACTGGAGAGTCTAMapped 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|164050575|gb|ES200962.1|ES200962EST: ATCGTGTCAAAGAGCTGCGTGAAATAATACCAAACGGTGCAAAA TGTAGCATTGATGCACTCC
genomic: ATCGTGTCAAAGAGCTGCGTGAAATAATACCAAACGGTGCAAAAgtaagtgaaa ... tatttaacagTGTAGCATTGATGCACTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatccctaagaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA
tactaac putative branch site (score: 0)
tttttattt putative PPT
tttttatttaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaaaaacttatctgttcttggcaaattaaacaatccctaagaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA