Sequence
atgc intronic sequence ATGC exonic sequencegtaaatatgatactttcttttattttgtagaactgatctttttgcaatttctcatgctgggctttttctttttgacagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66310.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 5
------------gtaaatatgatactttcttttattttgtagaactgatctttttgcaatttctcatgctgggctttttctttt------tgacagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
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gttacctttttccttgacatggt-ttgctgattaccttcaacaa--aaatcctgcaaaatttatcacattttgctgttctttctgaatgcaaacagAAAGGAACAGTTGTAGAAAAACTCACCGAGGAGACTCTGCGAGACAAAGGCCATCTTCTGGAGCTCCTTGCTGTGTGTGAAG
upper sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 4
gtaaatatgatactttcttttattttgtagaactgatctttttgcaatttctcatgctgggctttttctttttgacagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
|||||||| | | | || ||| | | ||| | || | || ||| | | ||| ||| ||||||||||||||||||||||| |||||||||||||||| | | |||||||| ||||| | || || | || ||||| |||
gtaaatatctttatcagtgtt-tttcaaaaagctggtgcttctacattttacttaacag---tttgcaatttaaacagAAAGGGACAGTTGTTGAGAGACTCACAGAGGAAACTTTAAGGGACTGGAACCATTTTCAAGAACTTATTTCATTCTGCGAAG
upper sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 4
gtaaatatgatactttcttttattttgtagaactgatctttttgcaatttctcatgc----tgggcttt--ttct---------------------------------ttttgacagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
|||||||| | | |||| ||| | ||||| | || | || ||| | | || ||| |||| ||| ||||||||| ||||||||||||| |||||||||||||||| | | || |||| ||||| | || || | ||| ||||| |||
gtaaatatctttatcagttttttttcaaaaaactggtgcttctacattttaccgaacaatttgcaatttgcttctcaaagaaagaaaaaaaaaacttacagtttgcaatttaaacagAAAGGTACAGTTGTTGAGAGACTCACAGAGGAAACTTTAAGGGATTGGAGCCATTTTCAAGAACTTATTTCTTTCTGCGAAG
upper sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
gtaaatatgatactttcttttattttgtag-aactgatctttttgcaatttctcatgctgggctttttctttttga-cagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
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--------gttagttcccttctcaatgtaccaactagtatatttata-tttcaaatactgatggtccactatttaaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtagaactgatctttttgcaatttctcatgctgggctttttctttttgacagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
aactgat putative branch site (score: 3)
ctttttctttttgac putative PPT
tttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatatgatactttcttttattttgtagaactgatctttttgcaatttctcatgctgggctttttctttttgacagAAAGGGACAGTTGTTGAGAAACTCACAGAGGAAACTCTGCGAGACTGGAATCATTTCAAGGAGCTCCTATCTGTCTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG