Sequence
atgc intronic sequence ATGC exonic sequencegtaacacgttttgccaacatggctcttatttctatatctgattattaagacaattttgaaacttctttaaaatccagGTAAAAGCATTAGATTACTTGCATTCCAACCGTATAATTCACCGTGACATGAAGCCACAAAACATTCTTATTGGTGCTGGCTCTGTCGTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50240.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G22860.1 (Glycine max), 3'ss of exon 4
-------------------------------gtaacacgttttgccaacatggctcttatttctatatctgattattaagacaattttgaaacttctttaaa--atccagGTAAAAGCATTAGATTACTTGCATTCCAACCGTATAATTCACCGTGACATGAAGCCACAAAACATTCTTATTGGTGCTGGCTCTGTCGTTAAG
||| | ||| | | | | | || |||| ||| || | || || | ||| | || ||||||||||| ||| |||| ||||||||||| || || || || ||||| |||||||| ||||| ||||| ||||||||||| ||| | || |||
gtatttcctctaaaacatctttgctctgtttttaatagcatttagatgaagagatatgaaaa-taaatcttatt-ttggcagaagttcatttttggtttggattatgcagGTAAAAGCCTTACATTATTTGCATTCCAATCGGATCATCCATCGTGATATGAAGCCCCAAAATATTCTAATTGGTGCTGGATCTATTGTCAAG
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 4
-----------gtaacacgttttgccaa-----catggctctta--tttctatatctgattattaagacaattttga---aacttc--------tttaaa--atccagGTAAAAGCATTAGATTACTTGCATTCCAACCGTATAATTCACCGTGACATGAAGCCACAAAACATTCTTATTGGTGCTGGCTCTGTCGTTAAG
|||| ||| | ||| || ||| | | || ||| ||||| | |||||| || ||| ||| || || ||||||||||| ||| |||| ||||||||||| || || || || || || |||||||| ||||| ||||| ||||||||||| ||||| || |||
gtatttcctcttaaacatctttgctctgtttttcatagcatttagatgaggagatatgaagattaatattattttggcagaagttcatttttggtttgaattatgcagGTAAAAGCCTTACATTATTTGCATTCCAATCGGATCATCCATCGCGATATGAAGCCCCAAAATATTCTAATTGGTGCTGGATCTGTTGTCAAG
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------gtaacacgttttgccaa--catggctcttatttc-tatatctgattattaagacaattt--tgaaacttctttaa-------aatccagGTAAAAGCATTAGATTACTTGCATTCCAACCGTATAATTCACCGTGACATGAAGCCACAAAACATTCTTATTGGTGCTGGCTCTGTCGTTAAG
| | | ||| || | |||||| || || || ||| | ||| | || ||| | | | | ||||| | |||||| | |||||||| ||||||||||| || || || || |||||||||||||| ||||| ||||||||||| ||| | ||||||
gtactttcctaagtttcctcctggaatattgctctcatttcaaatactaatcatattcaatgtttaatgttgcaatgtgcagggttataatttctatttcatacattatgttcttatatcgttttattagaatttcctgatgttgaatatttcagGTGAGAGCATTGCACTACTTGCACTCCAACCGTATCATACATCGAGATATGAAGCCACAAAATATTCTCATTGGTGCTGGTTCTATTGTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttatttctatatctgattattaagacaattttgaaacttctttaaaatccagGTAAAAGCATTAGATTACTTGCATTCCAACCGTATAATTCACCGTGACATGAAGCCACAAAACATTCTTATTGGTGCTGGCTCTGTCGTTAAG
atctgat putative branch site (score: 4)
cttcttt putative PPT
aattttgaaacttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacacgttttgccaacatggctcttatttctatatctgattattaagacaattttgaaacttctttaaaatccagGTAAAAGCATTAGATTACTTGCATTCCAACCGTATAATTCACCGTGACATGAAGCCACAAAACATTCTTATTGGTGCTGGCTCTGTCGTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC