Sequence
atgc intronic sequence ATGC exonic sequencegttaagatttgtcatttggtgtccatttcccttgtgaaattttgagcgagctgcttggccgatactgaagcattgaaatgttgcagGAACTGAAGGGAAACATCCGTGTATTCTGTAGGGTGAGACCTCTATTATCAGGAGAGAATTCTAGTGAGGAGGCCAAAACTATATCCTACCCTACATCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27180.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 8
gttaagatttgtcatttggtgtccatttcccttgtgaaattttgagcgagctgcttggccgatactgaagcattgaaatgttgcagGAACTGAAGGGAAACATCCGTGTATTCTGTAGGGTGAGACCTCTATTATCAGGAGAGAATTCTAGTGAGGAGGCCAAAACTATATCCTACCCTACATCTC---
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gtagtgctcttacactggacttttgtttgg-ttgtggtacacagttcttataccttgctatctttctaaactttcttataatgcagGAACTTAAAGGAAACATCCGTGTATTCTGTAGAGTGCGGCCTCTATTGGC---AGATGACTCTGCTGCAGAAGCAAAGGTCATTTCTTATCCCACTTCAACAG
upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33133 (Selaginella moellendorffii), 3'ss of exon 8
gttaagatttgtcatttggtgtccatttcccttgtgaaattttgagcgagctgcttggccgatactgaagca--ttgaaatgttgcagGAACTGAAGGGAAACATCCGTGTATTCTGTAGGGTGAGACCTCTATTATCAGGAGAGAATTCTAGTGAGGAGGCCAAAACTA--TATCCTACCCTACATCTC
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--------------------------------------gttcgcacttttctgtttttatcac-ctaaggcaaacagtgatgttacagGAGCTGAAGGGGAACATTCGTGTATTCTGTAGAGTAAGACCACTTTTACCCGATGAAAACGACGAATCATCGACTCTGATCAGCTATCCAGGCGAGGAGG--
upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ27367 (Selaginella moellendorffii), 3'ss of exon 7
gttaagatttgtcatttggtgtccatttcccttgtgaaattttgagcgagctgcttggccgatactgaagcattgaaatgttgcagGAACTGAAGGGAAACATCCGTGTATTCTGTAGGGTGAGACCTCTATTATCAGGAGAGAATT-CTAGTGAG-GAGGCCAAAACTATATCCTACCCTACATCTC
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---------------------------------gttcgcgcttttctgtttttatcacctaaggc--aaacagtga--tgttacagGAGCTGAAGGGGAACATTCGTGTATTCTGTAGAGTAAGACCACTTTTACCCGATGAAAACGACGAATCATCGACGCTGATCAGCTATCCAGGCGAGGAGG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgaaattttgagcgagctgcttggccgatactgaagcattgaaatgttgcagGAACTGAAGGGAAACATCCGTGTATTCTGTAGGGTGAGACCTCTATTATCAGGAGAGAATTCTAGTGAGGAGGCCAAAACTATATCCTACCCTACATCTC
aaattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaagatttgtcatttggtgtccatttcccttgtgaaattttgagcgagctgcttggccgatactgaagcattgaaatgttgcagGAACTGAAGGGAAACATCCGTGTATTCTGTAGGGTGAGACCTCTATTATCAGGAGAGAATTCTAGTGAGGAGGCCAAAACTATATCCTACCCTACATCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG