Sequence
atgc intronic sequence ATGC exonic sequencegtaatatacaccactgttgttagtttgttctcattcctttaagctgttttaatcaaagttggtaattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G49640.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G49640.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g44890.1 (Oryza sativa), 3'ss of exon 5
----gtaatat-acaccactgttgttagtttgttctcattcctttaagctgttttaatcaaagttggtaat--tgattcctccttccttaaaa--tacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
|||| | | | | | | ||| || | ||| | | |||| | | ||| | |||| |||||| | | | ||| || | |||||| ||||||||||||||||| |||||||||||||||||||| ||| | ||| | || ||||| || || || ||||| ||||| ||
cagaataatgtcatatatcaactctccattttcaatcttccctaatatgtctttttttgttaattgatttccctgatgttggattcctttacacatgcagAAAGGTCAAAGACAGACCAAGAGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGTCTGCACTGTCAATTCCAGTTATAGCTAATGGAGATGTATTT
upper sequence: AT3G49640.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G23820.3 (Glycine max), 3'ss of exon 5
--gtaatatacaccactgttgtt-agtttgttctcattcct----ttaagctgttttaatcaaagttggt--aattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
| | | | | | |||| | ||| | | || || |||| || | | || || || | || ||||| || | | ||||| ||| | |||| ||||| |||||||||||||| ||| |||| || || ||||| ||| |||||||||| ||||| || || |||||||| ||||||||
taattctctctcctatttctgttcaatttcatttaatcactaatattaatctttggttattaacacatgttcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGCAAATGGTGATGTTTTT
upper sequence: AT3G49640.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G36840.1 (Glycine max), 3'ss of exon 5
gtaatatacaccactgttgttagtttgttctcattc---------ctttaagctgttttaatcaaagttgg--taattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
||| | || || | ||| | ||||| |||| || | | || || | | || ||||| || | | ||||| ||| | |||| ||||| |||||||||||||| ||| |||| || || ||||| ||| |||||||||| ||||| || || | |||||| ||||||||
--aattctttctcctattttctgttcaatttcatttaatcactagtattaatctttggttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
upper sequence: AT3G49640.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s2201g00010.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaatatacaccactgttgttagtttgttctcattcctttaagctgttttaatcaaagttggtaattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
|||| | | | || ||| | | | ||||| ||| | | | ||||| | || | | | | || | ||| | ||||||||| ||||| || ||||||||||| ||| |||||||||| ||||| || || |||||||| ||||| || || |||||||| ||||| ||
ttttattttaaaaaaataaaaaattatacaattgattttattatttccttttaaactgcataact---agttgtcacatgcattcctgatggatgaattgcagAAGAATTGCAGATAGGCCTAGGGATCCTGCTAAGTGGAATGAGATTGCTGATGTTGTAGCGGCATTATCTATTCCGGTTATAGCAAATGGTGATGTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaagctgttttaatcaaagttggtaattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
ttgattcctccttcct CT-rich tract
ttttaatcaaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatacaccactgttgttagtttgttctcattcctttaagctgttttaatcaaagttggtaattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG