Sequence
atgc intronic sequence ATGC exonic sequencegtaattttttgaaattgtttaagattaatgagactcacttctctctgttttgtgttttaatgtttggtttcctattcggttttcagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04040.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------gtaattttttgaaattg---tttaagattaatg-agactcacttctctctgt---tttgtgttttaat---gtttg------gtttcctattcggtt--ttcagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
| || |||| | ||| ||||| | || | || ||| | | | | ||| | || ||||| | || | | || | ||| ||||| | ||||| || |||||||||||||| || || |||||||||||||| |||||||||| ||||| ||||| |||||||||||||||
gtttgtcttagctgaattttatttctggtgtaatctaggtcttattaggaagcttttgttaatgaaatgatgttttcatgttgctttttaatttacatacaaggacatttccatttatgaatatgtacagtgatcctgtttgtgcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTAAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACTGCT
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------gtaattttttgaaattgtttaagattaatgag-actcacttctctctgttttgtgttttaatgtttggtttcctattcggtttt-cagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
|| | || | ||| || || | | || | | |||||| ||| | | ||| || || | || | ||| |||||| |||||||||| || ||||| |||||||| || || ||||||||||| || |||||||||| ||||| ||||| ||||||||||| ||
gttctatgaagggaaaaattacctttccatctgttcatctgttgtataatttgtttggcatacacatgagagaaaaattacctttcataaatatgcagctgttcctgtttc---tttaactatttctgtttaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
---------------gtaattttttgaaattgtttaagattaatgagactcacttctctctgttttgtgttttaatgtttggtttcctattcggtttt-cagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
|| | |||| || | | | | || | | |||||| | || |||||| ||| || | || | ||| |||||| |||||||||| || ||||| |||||||| || || ||||||||||| || |||||||||| ||||| ||||| ||||||||||| ||
taatttgtttggcatatacatgagagaaaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttg--ttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------gtaattttttgaaat-tgtttaagattaatgagactcacttctctctgttttgtgttttaatgtttggt-ttcctattcggtttt---cagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
|| ||||| | | || ||| | | | | | | | | || | |||| | | || || || ||| ||||| | ||||| || |||||||||||||| || || ||||||||||| || | |||||||| ||||| ||||| ||||||||||| |||
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 5
-gtaattttttgaaattgtttaag-attaatgagactcacttctctctgttttgtgttttaatgtttggtt--tcctattcggttt----------tcagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
|| | || ||||| || | | || ||| | | || || ||| || | |||| || |||| | | | |||| | |||||| |||||| ||| ||| ||||||||||| ||||| || ||||||||||| || |||| || || ||||| ||||| || |||||||||||
tgttaaattcagaaatctactatgtgatcatcagaataagaactgactctttagtaatcagtgatttgtttaactttatttgatctatctgacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactcacttctctctgttttgtgttttaatgtttggtttcctattcggttttcagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
tttcctattc CT-rich tract
ttttgtgttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttttgaaattgtttaagattaatgagactcacttctctctgttttgtgttttaatgtttggtttcctattcggttttcagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT