Sequence
atgc intronic sequence ATGC exonic sequencegtgcttcccgattcgcttttgtgccaaattattctcaactaaattcaattgtgagagtttttttggtttcatcctttttcagTTTACTTCTGTTTGTGAGCTTAAAGGCCACACGGACTGGATTCGGAGTTTGGACTTCTCATTACCGTTACACACAACAGAAGAAATACCCAATAGTATTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49540.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G25600.1 (Glycine max), 3'ss of exon 5
-----------------gtgcttcccgattcgcttttgtgccaaattattctcaactaaattcaa----ttgtg---agagtttttttggtttcatccttttt-------cagTTTACTTCTGTTTGTGAGCTTAAAGGCCACACGGACTGGATTCGGAGTTTGGACTTCTCATTACCGTTACACACAACAGAAGAAATACCCAATAGTATTA
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gtatctttatccgctaagttgtatattattaacttgaacttttggtttcttatagttttatctggcggcttgtgtttgaagttattttacttttcttttacatatgaacccagTTTGTACATGCATGTGAGCTAAAAGGGCATACAGATTGGATCCGGAGTTTGGACTTCTCATTACCTATAAGCATCAATGGGGAAGTAAACAATATTTTTC
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G41620.1 (Glycine max), 3'ss of exon 5
--------------------gt-gcttcccgattcg--cttttgtgccaaattattctcaactaaattcaattgtgagagtttttttggtttcatccttttt-------cagTTTACTTCTGTTTGTGAGCTTAAAGGCCACACGGACTGGATTCGGAGTTTGGACTTCTCATTACCGTTACACACAACAGAAGAAATACCCAATAGTATTA
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gtatcttcatcccctaagttgtagattattaacttgaacttttggtttcttgtagttttatctgtcggctggtgtttaagttattttacttttcttttacatatgaacccagCTTGTACATGCATGTGAGCTAAAAGGGCATACAGATTGGATCCGGAGTTTGGACTTCTCATTACCTATAAGCATCAATGGGGAAGTAAACAATATTTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattctcaactaaattcaattgtgagagtttttttggtttcatcctttttcagTTTACTTCTGTTTGTGAGCTTAAAGGCCACACGGACTGGATTCGGAGTTTGGACTTCTCATTACCGTTACACACAACAGAAGAAATACCCAATAGTATTA
aactaaa putative branch site (score: 2)
tttttttggtttcatc putative PPT
aactaaattcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttcccgattcgcttttgtgccaaattattctcaactaaattcaattgtgagagtttttttggtttcatcctttttcagTTTACTTCTGTTTGTGAGCTTAAAGGCCACACGGACTGGATTCGGAGTTTGGACTTCTCATTACCGTTACACACAACAGAAGAAATACCCAATAGTATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA