Sequence
atgc intronic sequence ATGC exonic sequencegttcttgtttctctttctacctatatcaagtttaaactttagatgatattggatatttgaatataatatattaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28500.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G44250.1 (Glycine max), 3'ss of exon 1
-------------------gttcttgtttctctttctacctatatcaagtttaaactttagatgatattggatatttgaatataatat--attaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG
|| | ||| |||| | ||| | | | ||||| | | |||||| | | | ||| |||||| || || | ||| || ||||||||||| ||||| ||||||||||| || |||||||| |||||||||||| | | || ||| | |||| ||||| || ||
ttgtttagttaatttgatctagctagattcattttccat-tatcttttgggtgttctttatgcaagaa-atatatttcattgtggtattgattaattattagGGTGG--TGGAATTCATGACTTGCCTGGACTGCCTGCTGGAGTGAAGTTTGATCCCACGGATCAAGAGATTCTTGAACATTTAGAAGCGAAGGTGCGATCTG---
upper sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G33460.1 (Glycine max), 3'ss of exon 1
-----------gttcttgtttctctttctacc--tatatcaagtttaaactttagatgatattggatatttgaatataat-------atattaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG
| |||| | | ||| | | | ||| | ||| | || | | |||| | ||||| | ||||||| | || | ||||| || ||||||||||| ||||||||||||||||| || |||||||| || ||||| ||| | | || ||| | |||| ||||| | ||
aattatagctaagttttgtctttattttttctattttattagatttggggcattcatttcaa-gaatatatatatatattttttttggtattaatttttagGCT--GCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG---
upper sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G36980.1 (Glycine max), 3'ss of exon 1
-------------------gttcttgtttctct-ttctacctatatcaagtttaaactttagatgatattggatatttgaatataatatattaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG
| |||| | | | || | |||| | | | | | | | | || | || | ||||||| || | ||||| || ||||||||||| ||||||||||||||||| || |||||||| || ||||| ||| | | || ||| | |||| ||||| | ||
acctaacgaattgtatctaacttttgtctttatattttttctattttattggggcattcatttcaagaataaacatctatattttg-gtattaattcttagGCT--GCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG---
upper sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G13710.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------------gttcttgttt--ctctttctacctatatcaagtttaaactttagatgatattggatatttgaata--taatatattaatatgtaatgtag-
|| | |||| || || | | | | | || | | |||| | ||||| |||| || | | | | |||| | | ||| || |||||||| || ||||| ||||||||||| || |||||||| |||||||||||| | | || ||| | |||| ||||| || ||
gttcttaattattaacctttttgttaatgatatatatcatatagataatattacccttttgagtactttttttttcttttgatgtaattgtcttagtttgattcatttttcatttttttttttggcgttctttatgaaaa-aattatttaaataaatattgtggtgttgaataattttagGGTGGTGGAATTCATGACTTACCTGGACTGCCTGCTGGAGTGAAGTTTGATCCCACGGATCAAGAGATTCTTGAACATTTAGAAGCGAAGGTGCGATCTG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaactttagatgatattggatatttgaatataatatattaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG
tattaat putative branch site (score: 2)
tttagatgatattgga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttgtttctctttctacctatatcaagtttaaactttagatgatattggatatttgaatataatatattaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG