Sequence
atgc intronic sequence ATGC exonic sequencegtaaattttcctgacgatactgagatttcgatactgaaatgaaaagtatttgtaattggtggaggtgtgatgcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G80350.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
-----------------------------gtaaattttcctgacgatactgagatttcgatactgaaatgaaaagtatttgtaattggtggaggtgtgatgcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
||| || | | | | | || | || ||| | | ||| |||| | || ||||| |||||| ||||||||||| || ||||||||||| || ||||| |||||||| || ||||| || ||||||| || ||||||||||||||||| ||
tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagttgtagttatgt--tgagatctgattg-aattcacttttacttaat-cagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGTAGCCGT
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 4
-----gtaaattttcctgacgatactga-gatttcgatactgaaatgaaaagtat-ttgtaattg-gtggaggtgtgatg-------------------cagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
||| || ||||| ||| ||| | ||| | | | || | | | ||||| || || ||| | |||| ||||| |||||| ||||||||||| || ||||||||||| || ||||| |||||||| || ||||| || ||||||| || |||||||| |||||||| ||
tgcttgtacatgttcct--tgattctgttgggttcacttttaatttgtattatctcttgtagttatgttgagatctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAGGATGGTAGCCGT
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
--------------------------------------gtaaattttcctgacgatactgag----atttcgat--actgaaatgaaaagt--atttgtaattggtggaggtgtgatg-cagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
| | || ||| | | |||| || |||| | |||| | | | |||| || | | ||||| |||||| |||||||||||||| ||||||||||| || ||||| |||||||| | ||||| || | |||| | |||||||||||||||| |||
gtaagtcaatcttcttcttcatggggcatgtatgcttcatcttctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGC
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
gtaaattttcct--------gacgatactgagatttcgatactgaaatgaa--aagtatttgtaatt-ggtggaggtgtgat-----gcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
|| ||| ||| | | | | | | ||| |||| | ||| || | | ||| || ||| | | | ||||| |||||| |||||||||||||| |||||||| || || ||||| |||||||| || ||||| || | |||| | |||||||||||||||| ||
gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgtcacgaaagaatgaaccatgattcagttgagttctttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagatttcgatactgaaatgaaaagtatttgtaattggtggaggtgtgatgcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
aaatgaaaagtatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattttcctgacgatactgagatttcgatactgaaatgaaaagtatttgtaattggtggaggtgtgatgcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG