Sequence
atgc intronic sequence ATGC exonic sequence...gaatcaatagatctgcactttaagtttgtgtgtttaacatcatctttctttggctatgtagtagctcttgattttgttgtttttgtcttgtttgtcccagGGTGATCCTCTTTATGTTAAAGTTAACAAATTGTCGTCCACAAAGACTCAACTTCCTTATGACTACTACTACCTGAATTACTGTAAGCCTCCTAAGATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13772.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13772.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 1
gaatcaatagatctgcactttaagtttgtgtgtttaacatcatctttctttggctatgtagtagctcttgattttgttgtttttgtcttgtttgtc-ccagGGTGATCCTCTTTATGTTAAAGTTAACAAATTGTCGTCCACAAAGACTCAACTTCCTTATGACTACTACTACCTGAATTACTGTAAGCCTCCTAAGATCT
|||| | | | ||| ||| || | | | | | || | || || | ||| ||| || || || ||| || | ||||||||| || || | ||| ||||| ||||| || || ||||| |||||||||||||| ||||||||||||| | |||| || || || || ||||| |
ttatcatttcaatttgtttttgctgctgttatttggtttttaattgtgtgtgtgtttgaagaatgaagatattgagttattgtt-tcatgtgtggcaccagGGTGACCCCCTCTCTGTCAAAGTGAACAAGTTATCATCCACCAAGACTCAACTTCCATATGACTACTACTTCTTGAAGTATTGCAAACCCAAAAAGATAT
upper sequence: AT3G13772.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 1
gaatcaatagatctgcactttaagtttgtgtgtttaacatcatctttctttggctatgtagtagctcttgattttgttgtttttgtcttgtttgtc---ccagGGTGATCCTCTTTATGTTAAAGTTAACAAATTGTCGTCCACAAAGACTCAACTTCCTTATGACTACTACTACCTGAATTACTGTAAGCCTCCTAAGATCT
| | || | ||| ||| ||||| ||| |||| | | | | ||| ||| ||| |||| | | ||| ||||||||| || || | ||| ||||| ||||| || || || || |||||||||||||| ||||||||||||| | |||| || || || || | ||| |
-attttattatttaattttttttcgctgt-tgttttttgctttctaattttgtgtgtttgaagattgaagatattga-gttattgtttcatgtgtggcaccagGGTGACCCCCTCTTTGTCAAAGTGAACAAGTTATCATCTACCAAGACTCAACTTCCATATGACTACTACTTCTTGAAGTATTGCAAACCCAAAACGATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttggctatgtagtagctcttgattttgttgtttttgtcttgtttgtcccagGGTGATCCTCTTTATGTTAAAGTTAACAAATTGTCGTCCACAAAGACTCAACTTCCTTATGACTACTACTACCTGAATTACTGTAAGCCTCCTAAGATCT
tcttgat putative branch site (score: 4)
tttttgtcttgttt putative PPT
attttgttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatcaatagatctgcactttaagtttgtgtgtttaacatcatctttctttggctatgtagtagctcttgattttgttgtttttgtcttgtttgtcccagGGTGATCCTCTTTATGTTAAAGTTAACAAATTGTCGTCCACAAAGACTCAACTTCCTTATGACTACTACTACCTGAATTACTGTAAGCCTCCTAAGATCT
gaatcaa
- - - - - - - - - - - agtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttttg