Sequence
atgc intronic sequence ATGC exonic sequencegtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G45332.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 11
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
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-----gtatct-acttttctattttcaagaatgctatattaa--ctttaataccatac-atgtgacaaataattaa---ttaaaataacatttcagTTTTCAAAGGCTCTGAATCGTTTCCAGAAAGAGGATCCTACTTTCCGTGTAGGTCTGGATCCAGAAAGTGGAGAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaa-tctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
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-----gtatatcatatttttcatcaaaagggtacgactgctatacat-agtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctatttt--ccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
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gtgagtaatttattttatgtaac-acgtcaaccccctgcctagatttgaaaaaagttgtatcacct----aattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 11
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
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-------gtgagtacggccaa-ttgagatatcaa-----tttactttgtaactgatggtaccaaat----gatggtaattttttatccttgtacagTTTTCAAAGGCTTTGAATCGCTTTCAGAGAGAGGATCCTACTTTCCGTGTTGGGTTGGACGCTGAGAGTGGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
ctttaat putative branch site (score: 4)
tctattttcc putative PPT
aaatctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT