Sequence
atgc intronic sequence ATGC exonic sequencegtgagttggagaattctgtatctgctcctgattttgtgagatatataaacgagaggttgtatcactaattgctgttatctttttatagGTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 2
gtgagttggagaattctgtatctgctcctgattttgtgagatatataaacgagaggttgtatcactaatt------gctgttatctt--ttta-------tagGTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG
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gtgagtgagtgaatggaccaa--gcttttatgtttttaacataaataacttgcctttttcgttgctggtttggtttgttgagattttggtttggtgatatcagGTGAGAGGAGCTGTTACGATGAAGGGAAGCGGACTGCGGAGACATTGGCCATGGATTATCATCGAGGAGCTGGTGTTGAG
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtgagttggagaat-tctgtatctgctcctgatttt--gtgagatatataaacgagaggttgtatcact--aattgctgttatcttttta-----tagGTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG
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gtgagaactgataatttcttaacaaatgtttatgctttttgttgtctgttaataggttctgtatgcctgtggcatttttgtttcaaatgtttaaatacttgaactgattagGTGTGAGGAGCTGCTATGATGAAGGAAAACGTACAGCTGAAACTTTGACAATGGATTATCATAGAGGTGCTGAAGTTGAG
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------gtgagttggagaattctgtatctgctcctgattttgtgagatatataaacgagaggtt-gtatcactaattgctgttatctttttatagGTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG
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gggtatgtaggttgatgactaaagatttttcaggggtgcacttttcgccgtg-gttgtggaggttggatttttgtctcagcagtg--tgacgtttgtgtgcagGTGTTCGTAGTTGTTATGATGAAGGAAAGCGTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgagatatataaacgagaggttgtatcactaattgctgttatctttttatagGTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG
cactaat putative branch site (score: 2)
ttatcttttt putative PPT
tgttatctttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttggagaattctgtatctgctcctgattttgtgagatatataaacgagaggttgtatcactaattgctgttatctttttatagGTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG