Sequence
atgc intronic sequence ATGC exonic sequencegtatacccctttgcgtgaattgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43310.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43310.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g26440.2 (Oryza sativa), 3'ss of exon 6
-----gtatacccct---ttgcgtgaattgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
||| | | | || | | | | ||||| | | | | | | || || ||||| | || | | |||| || | || ||||| ||| | ||| ||| || || || || || | | || |||||| || | ||||| ||||||||||||||||||||||| ||||| ||
tacatatatgctctaagatcgcattcagtttcttttgatacttacctgtcctacatgggga-agctgttaa-cagatacattctcttatgaacaact-ta-cagAGTCCAACTGCTGAGAGTGCTTGAAACCCGAAAAAATGTCTTAAGGAAAGAGCAGGCTATGGCTTTTGCACGTGCTGTGGCAGCTGGGTTTGACATCGAC
upper sequence: AT5G43310.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G00690.1 (Glycine max), 3'ss of exon 7
-----------------gtatacccctttgcgtgaattgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtg-----------gaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT-------
| | || ||| | | ||| || | | || ||| || ||||| |||| | ||| | | | | ||||| | ||| ||| || ||||||| ||||||||||| || ||| |||||||||| ||||||||||| |||||||||||||| || || |||||||| |||
gttcacatatgtagaatcggtgctttttaaagtgttgtactcgttgagcatctgt-tcattgtgtaaaattggttgttaa-catctgtgttgtattgtattcccttctttatgtattgttttagacttcagCTTTTGAAAGTCCTGGAGACACGTAAATCTATGCTGCAGAAAGAGCAAGGAATGGCATTTGCACGTGCTGTTGCTGCGGGTTTTGACATTGACTACATGA
upper sequence: AT5G43310.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G00660.1 (Glycine max), 3'ss of exon 8
-------gtatacccctttgcgtgaattgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
|| | ||| | || | | | || || | || || | | | | | ||||| ||||| | |||| ||| || ||||||| ||||||||||| || || |||||||||| ||||||||||| |||||||||||||| || || |||||||| |
ctttttaaaatgttgtactcattgagcatctgttcgttgtgtaaaattggttgttaacatctgtgttgtattgtattcccttctttatgt---attgttttagAGTTCAGCTTTTGAAAGTCCTGGAGACACGTAAATCTTTGCTGCAGAAAGAGCAAGGAATGGCATTTGCACGTGCTGTTGCTGCGGGTTTTGACATCAAC
upper sequence: AT5G43310.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G35020.1 (Glycine max), 3'ss of exon 6
----------gtatacccctttgcgtgaa--ttgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
||||| | || ||||| || ||| ||| |||| || | ||| ||| | | | || | || | |||| ||||| |||| ||| || ||||||| || || ||||| ||| | ||||||||||| ||||| ||||| ||||| |||||||| || ||||||||||| |||
tgagctgcttgtatataaatatg-gtgaagtttatttattgagtttctttgcactatgtgaaacagattgttaactcattcactt--ctacatgt-----tgtattagAGTTCATCTTCTGAAAGTCCTAGACACACGTAAGTCAGCATTGCAGAAAGAGCAAGGCATGGCATTTGCTCGTGCTGTTGCTGCTGGTTTTGACATTGAC
upper sequence: AT5G43310.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G32560.1 (Glycine max), 3'ss of exon 10
gtatacccctttgcgtgaattgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT-------------------------
|| ||| |||| ||| || ||||||| || |||||||| ||| | ||||||||||| ||||| ||||| ||||| |||||||| || ||||||||||| |||
--------------------------------------------------------------------------------------gttctattagagttcatcttctgaaagtcctagagACACGTAAGTCAGCATTGCAGAAAGAGCAAGGCATGGCATTTGCTCGTGCTGTTGCTGCTGGTTTTGACATTGACTATATACCGCCTTTGATGTCATTTG
upper sequence: AT5G43310.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0049g01280.t01 (Vitis vinifera), 3'ss of exon 6
-----gtatacccctttgcgtgaattgtt--ttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
|| | | | | || || | | | | | ||| | | | || | | ||| ||||| | || | || ||| ||||||| ||| || | ||||| ||||| ||||| || | || | |||||||| ||||| ||||| ||||| |||||||| || ||||||||||| |||
gcttgctacatctacctatatcttttattcatctcaataattcaaacgcttctgccatagtattaat--attatataattttttatttatgctatta-atcagAGTTCAGCTTTTAAAAGTCCTGGAAACACGCAAAACTGTGCTTCAGAAAGAGCAAGGGATGGCTTTTGCTCGTGCTGTAGCTGCTGGTTTTGATATCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
atctaat putative branch site (score: 3)
ttaagtatctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacccctttgcgtgaattgttttttggttttcaatgtttttcaacaaagagagtagttaagtatctaattggtaatatgtggaattgtatcagAGCTCAAGTTATGAAAGTTCTGGAGACACGGAAGATAATGTTGCAGAAAGAACAAGGAATGGCCTTTGCACGTGCTGTGGCAGCTGGTTTTGAGGCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT