Sequence
atgc intronic sequence ATGC exonic sequencegtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41740.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 6
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
||| | ||| || || || || | ||| || || ||||||| | | | | |||||| |||||||| | |||||||||||||||||| ||| ||||| || ||||| |||||||| ||||| || | ||||| | ||| ||||| |
---------------------------------------gtatgctcgacaaccaaat-ctcaattcatgtaactttctggcacaaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G32100.1 (Glycine max), 3'ss of exon 4
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
| || ||| | | || |||| ||| | ||| | | |||| ||| | ||| || || | || ||| | || ||||||| ||||||||||| || || ||||| || |||| ||||||||||||||||||||||||||||| || || | ||| || | ||| ||||| ||
------------------gtaaggcaatttttctattatgtattc-cagtatttctgttcttcatctgcaattttt-tgttt------ttaacttcataaaatctatcccac-attccagATGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAGTTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
| || ||| | | | || |||| ||| | ||| | | || | ||| || || || | || ||| | || |||| || ||||||||||| || || ||||| || |||| |||||||||||||||||||||||||||||| || || | ||| || || ||| ||||| ||
------------------gtaaggcaattttcctattatgtattt-cagtatttctgttcttccaatgcacattc-atttgtt----ttttacttcataaaatctatcccac-attgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 5
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacag--tgttttaatacttaaagaataggttt------tgtgtgtggaaacttatctatattcatac-----tttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
|| |||| | | |||||| ||| | ||||| || || | | || | ||| ||| ||||| | | || | | | ||| | ||| | || ||||||| ||||| | ||||| || ||||| || |||| ||||||||| |||||||||||||||||||| || || | ||| | | ||| ||||| ||
-----gtaagggcacaaggcacat-gttttcctgtaacttgatgaaaagcttgccatgtgattttgaatatatgttctccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccac-attgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 6
gtaag--ccaattgcac---cttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatac-----tttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
||||| | || |||| || | ||| || ||| | | | | ||| |||| | | | || |||| | | || | | | ||| | ||| | || ||||||| || || | ||||| || ||||| || |||| ||||||||| |||||||||||||||||||| || || | ||| || | ||| ||||| ||
gtaagggcaaaaggcacatgttttcccatcacttgatgaaaagcctaccatgtgattttgaatatatgatctccaagt---gtgtattttgatttgtttgtgactataaaaaggtgtcccac-attgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
ctttcctgct CT-rich tract
aaacttatctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA