Sequence
atgc intronic sequence ATGC exonic sequencegtaagttatctagtatttgagtttaggattccgaggcttaaaaaatgtgttcttgatggttgctggttgttgtgctatagGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g51540.1 (Oryza sativa), 3'ss of exon 3
-----------gtaagttatctagtatttgagtt--taggattccga--ggcttaaaaaatgtgttcttgatggttgctggttgtt-----gtgctatagGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATAC
|| | || || | | ||| || ||| || |||||||| ||| | || | || | | ||||||||||||| || ||||| || |||| || ||||||||||| || ||||| ||||| |||||||| || | ||||||||||| || || || |||||
aagtcaacatcgtcatacatttataaatagagggagtatcattgttgctaattttaaaaatgtaactttgctactttttttgtggtcaaacatctaatagGTATTATGGAGGATGGGCAGCACCCAACATCTACTTTTTGGGGTTCGCTGGTGTTGTTAAGTTTGGAAACATTCGAATTGGTGGACTATCAGGAATATAT
upper sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 4
----------------gtaagttatctagtatttgagtttaggattccgaggcttaaaaaatgtgttcttgatggttgctggttgttgtg-ctat-----agGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATAC
||| || | ||| || || || || | | | || ||| | ||| ||| || |||| ||||| ||||| || ||||| || | || || ||||||||||| |||||||| ||||| |||||||| || | ||||||||||| | || || ||| |
caagaagattaacaatgtactttgagcaacctttcggtgctttatctatag--ttgatgtttttttttttgctcattggaaaatgtaatgactatttatcagGTACTATGGAGGATGGGCAGCACCTAACATATACTTTTTGGGGTTTGCTGGTGTTGTTAAGTTTGGAAACATACGAATTGGTGGATTGTCAGGAATACAT
upper sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaagttatctagtatttgagtttaggattccgaggcttaaaaaatgtgttcttg---atggttgctggttgttgtgc-----tatagGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATAC
|| | |||||| || | ||| ||| || | | || || ||| || ||||| | | |||||| ||||| || ||||| || | || || ||||| ||||| ||||||||||| ||||||||||| ||| | || |||||||| || ||||| || ||
ataaatttaggtttcaaaatgtctagtggtt-actttgtgatattttattctagatggttgacgtatgtacatcgttactatgtgttggccacatttttagGTACTATGGAGGATGGGCAGCGCCTAACATATACTTCTTGGGGTTTGCTGGAGTAGTCAAGTTTGGAAATATTCGTATTGGTGGGCTCTCTGGAATTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattccgaggcttaaaaaatgtgttcttgatggttgctggttgttgtgctatagGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATAC
tcttgat putative branch site (score: 4)
ttaaaaaatgtgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttatctagtatttgagtttaggattccgaggcttaaaaaatgtgttcttgatggttgctggttgttgtgctatagGTATTATGGGGGTTGGGCTGCCACCAATATTTACTTTTTGGGTTTTGCTGGAGTTGTCAAGTTTGGTAATGTGCGAATTGGTGGCCTTTCTGGTATATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG