Sequence
atgc intronic sequence ATGC exonic sequencegtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G137286_T02 (Zea mays), 3'ss of exon 2
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
| ||| || || | | | | | ||| || | ||| || | ||| || |||| ||| | || | | || ||||||| |||||||| ||||||||||| ||| |||| || ||||| ||||| || ||||||||||| || | |||||||| || || |||||||| | |
----------------------------------------------gtttgtgaaa--gtctatcttctatcctattttatcaattatcttttaca--------ttttgatctttacctgacaa--tgctggcacgcttcatgaatggccctagGTAGTTGAAGATGGTTATGAGTTTTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTACTGTGGAGAGTTCGATAACGCCGGTGCTCTGT
upper sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
| ||| || || | | | | | | | || | | | | | || | || |||| ||| | || | | ||| |||| || |||||||| |||||||| || ||| |||| || ||||| ||||| || ||||||||||| ||| | ||||||||||| |||| || || | |
----------------------------------------------gtttgtgaaa--gtctatcttctatcctgttttatcagt-tatttttggtt-------ctctgatctttacctgacaa--tgctggcacgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
upper sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G42050.1 (Glycine max), 3'ss of exon 2
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
| | || | | | || || ||||| | || || | | | || || | || | ||| || || || | | || |||| ||||| ||||| ||||||||||| || ||| | || |||||||| ||||| || |||||||| ||||| || || ||||||||||| ||||| || |
-----------------------------------------ttccttgctttcttact--ttaacctttgtc---ttttatgtgtt---acttcttccaacttcctctgatcaaggcctc-----attttactttcctattttttttttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTATGGTGGGGAATTTGACAATGCTGGTGCGTTGT
upper sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 2
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgt-tgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
||| | ||| || || | | |||| | | | | || || || | | | || || || | | | | | || |||| ||||| ||||| ||||||||||| || ||| | || |||||||| ||||| || |||||||| || || || || ||||||||||| |||||||| |
----------------------------------------------atcttccctgcttttttactttaacctttgtcttttatgtgtta-cttattccaacttcctctggtcaaggtct--cattttactttcctat------tttcttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTACGGTGGGGAATTTGACAATGCTGGTGCATTGT
upper sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
| | | | || ||||| | || | | | | | | | ||| | | || | ||| | | | || | |||||||| ||||| ||||| ||||| || || || ||||| | ||||||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| | |
---------------------------------------------------tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatacta--aaaacaagtggtccagac-taaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
tattgac putative branch site (score: 2)
ttttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA