Sequence
atgc intronic sequence ATGC exonic sequencegtaaccacagactctacttattgaagctatgatgaaacttaccacgatgaagaaataacaattcctttcattctacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G14650.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G14650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
--------------gtaaccacagactctacttattgaagctat--gatgaaactt----accacgatgaagaaataacaattcctttcattc--tacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA
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aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtaatttttggtcgaatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: AT5G14650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
--------------gtaaccacagactctacttattgaagctat--gatgaaactt----accacgatgaagaaataacaatt--cctttcattctacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA
| | | || ||| | ||| || || | ||| | || | || | || || | | || | |||| |||||||| | || |||||||| |||||| ||||| || |||||| |||| | ||||| |||||||||||||| ||||||||||| || ||
aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtattttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: AT5G14650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtaaccacagactct--acttattgaagctatgatgaaacttaccacgatgaagaaataacaattcct--ttcattctacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA
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gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatca-gtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagctatgatgaaacttaccacgatgaagaaataacaattcctttcattctacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA
aaataac putative branch site (score: 2)
ttcctttcattctac putative PPT
aagaaataacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccacagactctacttattgaagctatgatgaaacttaccacgatgaagaaataacaattcctttcattctacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA