Sequence
atgc intronic sequence ATGC exonic sequence...accattaacatgaaaaaaaaagcattacactaaaatttaaaagaaaaataaaaacattttcacaagtattaattaaccaacatttttcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23940.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G24900.1 (Glycine max), 3'ss of exon 1
accattaacatgaaaaaaaaagcattacactaaaatttaaaagaaaaataaaaacattttcacaagtattaattaaccaacatttt-tcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
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-tagtgcaccccactgatcacctatcacattcactctctcttttattattttctgtttttcatcttctaactttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
upper sequence: AT5G23940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G29960.1 (Glycine max), 3'ss of exon 1
accattaacatgaaaaaaaaagcattacactaaa--atttaaaagaaaaataaaaacattttcacaagtattaattaaccaacatttttcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
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atcacc--tatcactctcgctttctctttttaaatcatatgatatctttttatttttatttttcatgttctcacttcatttgcattctattcttgctcgcagTTAACGAAGCTCAAAGATGGGCTTGCAATGGGCCTAGCATTCAACCATGCTGTCTTGGACGGTACTGCCACCTGGCAATTCATGACCTCATGGGCCGAGA
upper sequence: AT5G23940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g00870.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------accattaacatgaaaaaaaaagcattacactaaaatttaaaagaaaaataaaaaca-------ttttcacaagt-attaattaac--caacatttttcgtttcgcaa----cagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
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gtaacaatttatttatttatttattttctattaaaagtggtcatatgactttggtacaaaaggaatgatttcccaatagttgaaaagatggactagaacaaagtttgttgtcccaggttattcaactgcttcaactgtttttctgtcatgatccgcagTTCACCAAGCTAAGAGATGGCCTCGCAATGGGATGCGCGTTCAACCACGCTGTCCTCGACGGTACCTCCACGTGGCACTTCATGAGCTCGTGGGCCGAAAMapped 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|47831380|gb|CK121064.1|CK121064EST: ATGGGATCTTGAACTTGGAAGGACTTAGCAGACCACTCCTTGCTGTCCAG GTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCA
genomic: ATGGGATCTTGAACTTGGAAGGACTTAGCAGACCACTCCTTGCTGTCCAGgtatgatgac ... ttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaataaaaacattttcacaagtattaattaaccaacatttttcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
aattaac putative branch site (score: 2)
tttttcgtttc putative PPT
attttcacaagtatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accattaacatgaaaaaaaaagcattacactaaaatttaaaagaaaaataaaaacattttcacaagtattaattaaccaacatttttcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - aacatga
- - - - - - aaaaaaa
- - - - - - - - - - - - - acactaa
- - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaccaa