Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgcgtgatacgttgtgaatatggattcacatgaggattagttggaaagcttaataattacttttgtacttgtatagGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02260.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 7
----------gtgagttgcgtgatacgttgtgaatatggattcacatgaggattagttggaaagcttaataattacttttgt-acttgtatagGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
|| ||| | ||| || || | | | || | || | || || || || | | |||| |||||| | || |||||||| |||| |||||||||||| ||||| ||||| |||||||||||| || |||||||||| | |||||| || || |||||||| |
gtgagtcatgaagaaatgcttccctttttgccaa-atttacttaagtgcgtataacaaatcaatatttatgatggatccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTCGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
upper sequence: AT4G02260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 5
gtgagttgcgtg---atacgttgtgaatatggattc-acatgaggatta-gttggaaagcttaataattacttttg-------tacttgtatagGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
|||||| | || | | | ||| || | | | | || | | || ||| ||| | | | |||| |||||| | || |||||||| |||| |||||||||||| ||||| ||||| |||||||||||| | |||||||||| | |||||| || || |||||||| |
gtgagtcatgaaaaaatgcttcccttttgccaattttacttaattagtgtgtataacaactctatatttatgatggaaccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
upper sequence: AT4G02260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 5
gtgagttgcgtgatacgttgtgaatatggattcacatg----aggattagtt------ggaa--agcttaataatt-actt-ttgtacttgtat--agGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
||||||| | || | ||| ||||||| | | || | ||| || | || ||| ||| || |||| ||| | || || ||||||||||||||||||| |||| |||||||||||| || ||||| || |||||||| ||| | | |||||||| | ||||| ||||||||||| |
gtgagttatg-gaaattttgggaatatgttcttatttgtcacataatttattcttcctgcaattagcaatatagtttacttattgaattttcatttagGAATTGGATTGGGAGTCCATTGCTGCTGGATTACTGCACGACACTGTTGAGGATACGAATGTTGTCACTTTTGACAGTTTAGAAAGGGAGTTTGGTGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattcacatgaggattagttggaaagcttaataattacttttgtacttgtatagGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
gcttaat putative branch site (score: 4)
ttaataattacttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgcgtgatacgttgtgaatatggattcacatgaggattagttggaaagcttaataattacttttgtacttgtatagGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG