Sequence
atgc intronic sequence ATGC exonic sequence...aatacatttgcatgttgaaaaggttttgtttaatgtaggtcaaggtgacacttgaccaatggactccttgatcgcttgatgttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30400.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 9
aatacatttgcatgttgaaaaggttttgtttaatgtaggtcaaggtgacacttgaccaatggactccttgatcgcttgatg------ttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG
|||| | || | ||| | | || | | || | | ||| || | |||| || | ||| ||| || |||| || ||||| |||||||||||||| ||||| || ||||| |||||||||||||||||| | || || || ||
----tttttgtaaattaggctg--cttgatggaattacatgcaagtaatttataacctttgcaagttttgacttattaagagcctatctgaatttgtttttgatagGTCTTTGGGGTGTTATGTGAAGCTCAATATTTTCAGAATGTCATGCGTGTTGGTTACCGGTTAAGATCAACATTG
upper sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 9
---aatacatttgcatgttgaaaaggttttgtttaat--gtaggtcaaggtgacacttgaccaatggactccttgatcgcttgatgttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG
|| || | |||| |||| ||| | ||| | | | ||| | | ||| || | || | ||| ||| | || |||| || ||||| |||||||||||||| ||||| || ||||| |||||||||||||||||| | || || || ||
tacaagtttttaataaacaataaagatttttttttgtttgtaaattaggctgatctcta--tggtc-acttattaagagcctatc--tgaatttgtctttgatagGTCTTTGGGGTGTTATGTGAAGCTCAATATTTTCAGAATGTCATGCGTGTTGGTTACCGGTTAAGATCAACATTG
upper sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 9
------aatacatttgcatgttgaaaaggttttgtttaatgtaggtcaaggtgacac--ttgaccaatggactccttgatcgcttgatgttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG
||| || | | | | | | | || | | | || || |||| ||| | | ||||| | | ||| | | | || | |||||||| ||||| |||| ||||||||||||||| || ||||| |||||||| |||| |||| |||| || | ||
gctcttgatattactgt-tatgggcatgctctcattctac-tggatctttgtaacacaattggaagaagaactccac-actgattggtttaaacttt-----ctccagGTATTCGGGGTATTATTTGAAGCTCAGTATTTTCAGAATGTCATGCGTGTGGGTTTCCGGGTTAGATCAACTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacacttgaccaatggactccttgatcgcttgatgttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG
tgttgac putative branch site (score: 3)
cattttc CT-rich tract
acatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatacatttgcatgttgaaaaggttttgtttaatgtaggtcaaggtgacacttgaccaatggactccttgatcgcttgatgttgatgttgacattttcagGTATTGGGGGTTTTATGTGAAGCTCAGTATTTCCAAAATGTGATGCGTGTTGGTTACCGGCTTAGGTCTGCACTG
- - - - - - - - - - -ggttttg