Sequence
atgc intronic sequence ATGC exonic sequencegtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G18330.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
----------------------gtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
| ||| || || || | ||| | | | || | | | | ||| ||| | | || ||| ||||||||||||||||||||||| |||||||| ||||||||||||||| ||||||| ||||| || || |||||||| || || || || |||||||||||||
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgac---atctgtgtgatatttgttttta--cttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
upper sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
---------------------gtattaatgagttta-atttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
| || || || | ||||| | | ||||| || |||| | | | | ||| ||| | | |||||||||||||||||||||| |||||||| ||||||||||||||| ||||||| || || || || || |||||||| || || || |||||||||||||
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgt-----agGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
upper sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
|| | ||| | | | | || | || ||| | | || | ||||| | || |||| ||||||||||| ||||| |||||||| |||||||||||||| ||||||| || |||||||| || ||||| ||||| || |||||||| || ||||
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatc--tagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
upper sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
---------------gtattaatgagtttaatttacac-tttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatc-agGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
| | || | || ||| |||| || | ||||| | || | | | |||| |||| ||||||||||| ||||| |||||||| |||||||| ||||| ||||||| || |||||||| || ||||| || || || |||||||| || ||||
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
upper sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgt--aactgagttgttt---tttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
|| | | | | | | | | | | | | ||| | || | ||| ||||| ||| || |||||||| |||||||| ||||| || ||||| |||||||| || || ||||||||||||||||| | ||||| || |||||||| || || || ||||
aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatccggattgaaatgtttgtgtttgtttg-cagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
atgtaac putative branch site (score: 3)
ttttttattc putative PPT
ttgttttttattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT