Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttcatttactgatactattcatggaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23300.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttcatt-tactgatac---tattcatggaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
|| || | | | | ||| | ||| || | | || | ||||||| | |||| | | ||| | | ||||||||| || || | || | | ||||||| ||||| ||| | ||| ||||||||||||| ||||| |||||||| |||||||| |||||||||
gtaagtttgttctttagaatctttcaccaataatttcttatcacaaacatgata-catattta-aatgttgggctttttcaaacttcattattgtgattcatcttttctactatctggcagATGCTAAAGTTCAAAGATAACAATATTAACAATGAGGGAATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 4
gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttcatttactgatactattcatggaaattg-cagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
| | | |||| | | | || || | ||| || | | | || | ||| |||||||| ||||| | | || | | ||||||| || | ||| | ||| ||||||||||||| ||||| |||||||| |||||||| |||||||||
-----gtaagccttttgtcttgattcttttgtaagt-tgccctgaaattctttaatctaacccatctctactgtttggcagATGCTAAATTTCAAGGATAACAATATAAACAATGATGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
------gtaaggcagttactagatc-ttatgtgga-atagaggtgtgtgtccatcttca---tttactgatacta---ttcatggaaattgc------agATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
| | | | ||| | | | ||||| || | | || || | | | | | |||| | | |||||| |||||||||||||||| ||||||| | | |||||||||||||| | ||| | ||||||||||||||||||| ||||||||||||||||| |||||| ||
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 3
-------------gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttcattt-actgatactattcatggaaattgc------agATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
||| | || | | |||| || | || | || || |||| | || | | | |||||| |||||||||||||||| ||||| | | |||||||||||||| | ||| | ||||||||||||||||||| ||||||||||||||||| || || |||
acacattttacccataaaatcatcaccaaaacttaagtttctcacctaattgagagtattttaattttaacactatattccttcacaattgctctttcagATGCTTAATTTTCCAAACAACAATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATACCTCCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 3
------------------------------gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttca--tttactgatactattcatg---gaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
||| | | || | | | || || | | || | | | |||| || | |||||||| | ||| |||||||| || ||||| |||||||| | ||||||| ||||| || | | || |||||||||||||||||||||| ||||||||||| |||||||||
gtaagctagttactcctatctagtttggcactaaaataatcaccaaaacataaaactcttatatgactggaaaaagttgtaactttattgtttatattcatgattggtattacagATGCTCAACTTTCCAAACAATGTCATAAACAATGAAGGAAGACTTCGCAATGTTTTTGATGTTGGCTGTGGTGTTGCAAGCTTTGGAGGATATCTTCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 3
------------------------------gtaaggcagttactagatctt--atgtggaatagaggtgtgtgtccatcttcatttactgatactattcatg---gaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
||| | | || | | | | | | ||| || | | ||| | | |||||||| | ||| |||||||| || ||||| |||||||| | ||||||| ||||| || | | || |||||||||||||||||||||| ||||||||||| |||||||||
gtaagctagttactcctatccggtatggcactaaaataatcaccaaaacatgaaactcttatatgactggaaaaagttataagtttgtagtttatattcatgattggtatttcagATGCTCAACTTTCCAAACAATGTGATTAACAATGAAGGAAGACTTCGCAATGTTTTTGATGTTGGCTGTGGTGTTGCAAGCTTTGGAGGATATCTTCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
---------------gtaaggcagttactagatcttatgtggaatagaggtgtgt--gtccatcttcatttactgatactattcatggaa----attgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
|| | |||| ||| | || ||| | | | | | | || ||||| | | || || |||||||||||| |||||| | || || | | || |||| ||||| ||| |||| |||||||||||||||| |||||||| || ||||||| ||||||||||
tcttttcaagaccatgtttgacagt-gttagttgtttggtgcattctgattatttaaattcactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
--------------gtaaggcagttactagatcttatgtggaatagaggtgtgtg--tccatcttcatttactgatactattcatggaa----attgc-agATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
|| | |||| ||| | || ||| | | | | | | | || ||||| | || || || ||||| ||||||| |||||| | ||||| | | || |||| ||||| ||| |||| ||||||||||||||||||||||||| || ||||||| |||||||||
attttcaagaccatgtttgacagt-gttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 4
----------------gtaaggc-agttactagatcttatgtg---gaatagaggtgtgtgtccatcttcatttactgatactattcatggaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
| || ||| | ||| | | || |||| || || | | | | | | | | | | | | ||||||||||| ||| | |||||| | | ||||| | |||||| || ||||| | ||||||||||||||||||||||| || ||||||| ||||||||
gtcagtaccatgtttaacagagctggttgtttgatatagtctgtttatctagatttgcttggataaatcattatcttaacattccaatttgcattgccagATGCTTAACTTTTCAAACAATAATCTAAACAACGAAGGAAGGTTGCGGACAGTGCTTGATGTTGGCTGTGGTGTTGCAAGTTTTGGAGCATATCTTCTAT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 4
------------gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatctt--------catt-tactgatactattcatggaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
| | || || || || | |||| || ||| || | |||| | | | | | | | | | ||||||||||| ||| | |||||| | | ||||||| |||||| || ||||| | ||||||||||| ||||||||||| || ||||||| ||||||||
acttttaatggtgctggttgtttgatatattccatttatc-tagatttgcttgtatttcatggataaatcattatcttaacattccagtttgcattgccagATGCTTAACTTTTCAAACAATAATCTAAACAATGAAGGAAGGTTGCGGACAGTGCTTGATGTTGGTTGTGGTGTTGCAAGTTTTGGAGCATATCTTCTAT
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 4
------gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttc----------atttactgatactattcatgga----aattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
| | || || | |||| || | || || | | | ||| | | | | || ||||| ||| | | ||||||||| || ||| | |||||| | | ||||| ||||||||| | | || || |||||||||||||||||||||| || ||||||| |||||||||
atttcattttagggatttctggttctttggtaaattattttagtattttcttctactgcatggttgaagcaataattctatttgtggcttgtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACTGTTTTTGATGTTGGCTGTGGTGTTGCAAGTTTTGGAGCCTATCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaatagaggtgtgtgtccatcttcatttactgatactattcatggaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
tactgat putative branch site (score: 2)
ttcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcagttactagatcttatgtggaatagaggtgtgtgtccatcttcatttactgatactattcatggaaattgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG