Sequence
atgc intronic sequence ATGC exonic sequencegttaggtccttcctcttgatcttttgattttcttcttctccattgctctgatcaatcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 3
-------------gttaggtccttcctcttgatcttttgattttcttcttctccattgctctgatcaa---tcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
| | || | ||| | ||| | |||||| | | | | | || | || || ||||| |||| |||||||||||||||| | || ||||| |||||||||||| ||||||||| | ||||| || |||| | ||||| || || | |||
gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
upper sequence: AT4G39180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g03400.2 (Oryza sativa), 3'ss of exon 2
-------------gttaggtccttcctcttgatcttttgattttcttcttct--ccattgctctgatcaatcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
| |||| | ||| | ||| | || | | | | | | | | |||| || |||||| |||| |||||||||||||||| | || ||||| |||||||||||| |||| ||| | ||||| || |||| ||| ||||| || || | |||
gtgtataatctgaaaatagcacttcatgttgttatttagtttcaaatgtgaaaacaagtattactaaaattcgagattacacagGTTTTTGAAGGCAAGAAAGTTTGATGTTGAGAAGGCAAAGCAAATGTGGGCTGACATGTTGCGGTGGAGAAAGGAATTTGGTGCAGATACCATTCTTGAG
upper sequence: AT4G39180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G162461_T01 (Zea mays), 3'ss of exon 3
------gttaggtccttcctcttgatcttttgattttcttcttctccattgct-ctgatcaatcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
| || | || || |||||| | | | | |||| | | || || || | | |||||||||||||||| |||| ||||| ||||||||||||||||||||||| || ||||| || || | || ||||| || || | |||
gtatgtgatatagtaaaggattgtatgattgcattttcatgtgtggtagcattgctgaaagtttgggatcatgaagATTTCTCAAGGCAAGAAAGTTTGATATCGAGAAGGCAAAGCAAATGTGGTCTGATATGCTGAAGTGGAGAAAGGAGTTCGGTGCAGATACCATTCTCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgatcttttgattttcttcttctccattgctctgatcaatcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
ctctgat putative branch site (score: 4)
ttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggtccttcctcttgatcttttgattttcttcttctccattgctctgatcaatcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA