Sequence
atgc intronic sequence ATGC exonic sequence...actgcatgactgattctcagttatcattaaagttcattttatgtttaatatatatgctgatttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G38880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
---actgcatgactgattctcagttatcattaaagttcattttatgtttaatatatatgctgatttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
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ttaattctat--ccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatatttt-ttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
upper sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 4
actgcatgactgattctcagttatcattaaagttcattttatgtt-taatatatatgctga---tttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
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--tttaattctattcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccactt-attatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG-
upper sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0083g00990.t01 (Vitis vinifera), 3'ss of exon 4
actgcatgactgattctcagttatcattaaagttca----ttttatgtttaatatatatgctgatttacttgcttgaacaaacgatccgattt-tatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
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--tatccatctcatgcttgaaagttaatgtagcctgcatctattcttcctcatgtatatgctgatttgttt---tgtaagtattctctggttcatctttgtgcagTTGGAGGTATGGGCAAAGGAAAGAGAGGCGGCTGGATTGAGAGCAAGTTTGAATACCTTGATGTCTGAAGTGCAACGCTTAAATAAATTATGTGCAGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatatatgctgatttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
tgctgat putative branch site (score: 3)
ttttatcttt putative PPT
attttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgcatgactgattctcagttatcattaaagttcattttatgtttaatatatatgctgatttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
- - - - -ctgattc
- - - - - - - - - - - - cattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacga