Sequence
atgc intronic sequence ATGC exonic sequencegttgataccagctgatgtttttccaatatcttgcatcaaggagcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32440.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 4
gttgataccagctgatgtttttccaatatcttgcatcaaggagcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
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-----------------gttagttgatcccctgaccagtctagctg--ccatttagttgcatccaac--atcctaacgtgcttctgttttca-acagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 4
gttgataccagctgatgtttttccaatatcttgcatcaaggagcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
|| ||| || | |||| ||| | | || | | | || || || | |||| |||| || ||||||||||||||||||||||| || || ||| || |||||||| || || |||||||| |||||||| |||||| ||||||| || ||| |
-----------------gttagttaatcctctgactggtctagctg--ctatttagttgcatccaac--atcctaacatgcttctg-ttcca-acagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------gttgataccagctgatgtttttccaatatct-tgcatcaaggagcttttctaat---aaaatgtttttgagtggttat-attctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
||||||| | | | |||| | ||| | | | | | | | || ||| |||| | | | || ||| | | | | || |||||||||| |||||||| || || |||||||||||||||||||| |||||||| || || |||||||| || |||||| |||| |||||||||||||| |
gttatcttttgttcttatgttttttctaataggtgattttctgtttctattttccacgaagttgatatgatgtt-tcttttacttttatttgtctacttacgtgttatttgaattgtaaaaaatatccaatcttttcccattactcatgtcatttca-acagACAAAGACTGGGAAGATATCAAGTTTGGAGTGGACAACCAAGTTGATTTCTATGCTGTTTCCTTTGTGAAAGATGCTGAAGTGGTCCATGAGTTGAAAGA
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
gttgataccagctgatgtttttccaatatctt-----gcatcaaggagcttttctaataaaatgtttttgagtg--gttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
|| || | ||| || ||||| | || | ||| | | | |||| | || | || | | ||||| || |||||||||||||| ||||||||||| || || |||| ||||||||||| | || ||||| ||||| || | || || |||||| | ||
---aatttca-ttagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
ttttaac putative branch site (score: 2)
tctaataaaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgataccagctgatgtttttccaatatcttgcatcaaggagcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA