Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcttggttcttattcaagcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------gtatgtcttg--gttcttattcaagcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtatacc-acagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
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gtacgcagcatctttttgtgtaacatattcgtcatgttttcaagattttctggcttgcaatggattttcgttgtttccctgttttcttctgtttccaattgcatctgaatctagacccatgcttttcttatctgcagAGCTTGCAAGACGAGATGATGGATCTTATGGATGTGAGCAATGAAATACAGGAAACTCTCGGAAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAG
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
----gtatgtcttggttcttattca--agcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
|||| |||| | || | ||||||| | || | | | | | || | | | | || | ||| |||| ||||||||||| ||||||||| | ||||||| ||| ||||||||||||||| | ||||| ||||| ||||| ||||||||||||||||| ||||
gtatgtatctctttccttttctcttatagcttctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgt-gtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 4
gtatgtcttggttcttattcaagctt----ctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
|||||| || | | || ||| || | | | | | | | | | |||| || | || | |||| ||||||||||| ||||||||| | ||||||| ||| |||||| |||||||| | ||||| ||||| ||||| |||||||||||||| || ||||
gtatgtattccctttccttttctcttatagcttctatctaatctaatatcaaaatttttacgtcttaactgttgatccatgctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGATGAGGATG
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
----gtatgtcttggttcttattcaagcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
|||| ||| ||| | | | | | ||| | || | | || || | ||||| | |||| |||||||||| ||||||||| | ||||||| || || ||||||||||| | ||||| || || |||||||| || ||||||||||| || ||||
gtctgtattgctttaccgaggttctatgcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
ttaagaattatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcttggttcttattcaagcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG