Sequence
atgc intronic sequence ATGC exonic sequencegttagcattttatctaactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50250.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 2
---------gttagcattttatctaactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
|| | ||| ||| || | || || | | | |||| | | ||| | | | | |||| ||||| |||||||||||||||| || || ||||| || ||||| |||||||| || ||||| |||||||| |||||||||||||| ||||||||||| ||||| || ||
gtaaatcttgtcaccatattaacttgtgacttgagctgaaattatc--ctggtgtgcagaggttcctaatccatttttgaacttttcaatttgcagAGGCTGGTCATGCCCTTGTTGGTGCCCTCATGCCTGAATATGACCCTGTTGCTAAGATTTCCATCATTCCTCGTGGTCAAGCTGGTGGACTCACATTCTT
upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
---------gttagcattttatc-taactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaatttta-aatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
|| | || ||| |||| ||| || || ||| ||| || ||| || | | | |||| ||| ||||| ||||||||| ||||| || || || || || |||||||| |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||||| || ||
gtaaatgttgtcaaatttatattataaccataagtt-tgactcccgcttacggggctcaggttc-ctaatctgtt--gttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT
upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
gttagcattttatctaactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
|| ||||||| | || ||| | | | | || | | | | ||| | | | | |||| |||||||||| |||||||||||||||||| | |||||||||||||| || || || ||||| || || ||||||||||||||||||||||| ||||| |||||
gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
------gttagcattttatctaactatatgtaatggagtacgcagctgg--gattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
|| ||||| | | | | || || || ||| | | ||| | | | | | | | | |||| |||||||||| |||||||||||||||||| | ||||| |||||||| || || || ||||| || || ||||||||||||||||||||||| ||||| |||||
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 2
gttagcattttatctaactatatgtaatggagtacgcagctgggattcttgtt----ttctgaccacctcaa------atgaattt-----taaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
||| | ||| | | | |||| || ||| |||||| || || | || ||| ||| | ||||| |||||||||| ||||| | || ||||| |||||||| |||||||| || || || ||||| || |||||||| ||||||||||| ||||| || || |||||
--gtacataaaagagaacaacaca-agctttgtacaggtctctgatgcttgttattgttttgggtgttttaactctttatgtgtttgcacttgaatttgcagAGGCTGGGCATGCATTGGTCGGTGCACTTATGCCTGAATATGACCCTGTGGCCAAGATATCCATCATTCCCCGTGGCCAAGCAGGTGGTCTTACCTTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgcagctgggattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
ttctgac putative branch site (score: 2)
tcaaatgaattttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcattttatctaactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG