Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaaaaataattcagtcaatagatatgtttatcctcttataacgattttttcaagaaaaatttgttcatgaactttcagGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06550.3 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06550.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 12
-----gtaagtaaaaaataattcagtcaatagatatgtttatcctcttataacgattttttcaagaaaaatttgttcatga-------actttc----agGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG
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gctattttattgctaaatgctgtcaaatttaaatttcttcactttgttttgaggctggtaattagttaactaattttatgatgtttctactttcttgtagTTGGCTTGGGAAGATTACACTGGAGACTTATATCTCCCAGATCCATATCTGGTTAAG
upper sequence: AT3G06550.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 12
--------------gtaagtaaaaaataattca-gtcaatagatatgtttatcctcttataacgattttttcaagaaaaatttgttcatgaactttcagGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG
| | | || ||| | || | | ||| || | || | | |||||| | | ||| | || | | || |||||||||||||||||||||||||| || ||||||||| | ||||||||| | ||
gtaagtggccttggatttgaggatgttatttcctgcaaactattgtatttttcttgtttgaccaatttttgtgatat---tttatctttggtcccttagATGGCTTGGAAAGATAACACTGGAGACTTACATCTCCCAGATCCATATATGGTTAAG
upper sequence: AT3G06550.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S74_21V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------------------------------------gtaagtaaaaaataattcagtcaatagatatgtttatcc-tcttataacgattt--tttcaagaaaaatt--tgttcatgaactttcagGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG
|| ||| | | | | | | | | | ||||| | | || | || || || | | || || ||||||| | ||||| || || ||||||||||||||||| || ||||| |||||||||||
gtaagtatctcttggagatgttagatacttcgttttgtcctattttctgcatcagatttaaatgttagtatgtgtttcatgttcataagagagattgtgatgcttgtccgtactgaaatatcttaaatgggcttggtctccagctgctttactaattctgccattacagGTGGTTAGGAAAAATTACGCTGGAGACATATATCTCTCAATTTCACATATGGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttatcctcttataacgattttttcaagaaaaatttgttcatgaactttcagGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG
ttataac putative branch site (score: 2)
ctttc putative PPT
ttataacgattttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaaaaataattcagtcaatagatatgtttatcctcttataacgattttttcaagaaaaatttgttcatgaactttcagGTGGCTTGGAAAGATAACACTGGAGACATATATCTCCCAGTTTCATATATGGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA