Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacgatcttcttgattgatgtgtatgcatagctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14330.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G408308_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------gtaagaacgatcttcttgattgatgtgt------atgcatagctttatgcagcttatctctgt----tttaacttacta-gtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
|| | || | | ||| || | | ||| |||| | | | || | | | | || || | | | ||| | | ||||| || || ||||| ||| |||| || |||||||| |||||||| ||||||||||| |||||||| ||||| || || || || ||||||||||| |
gtggaaaaatgaagaactgtgaagagcacactttgcaatgagagaagttcacggagccattgcatggtttgttgcattcaaccaaccatcactttgaac-gttcatttttttaaaaccaagatttttacgaggtatactttgcatctatagATTATCCTGGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCA
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G150984_T02 (Zea mays), 3'ss of exon 2
gtaagaacgatcttcttgattgatgtgtatgcatagctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
| | | | | | | | | || || || | | || | | | ||| | | ||||| || || ||||| ||| |||| || |||||||| |||||||| ||||||||||| |||||||| ||||| || || || || ||||||||||| |
----gtttgttgcattcaaccaaccatcactttgaacgtt---catttttttaaaaccaagatttttacgaggtatactttgcatctatagATTATCCTGGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCA
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G062084_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------gtaagaacgatcttcttgattgatgtgt--atgcat-agctttatgcagc--ttatctct----gttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
|| | || | | ||| || | | || ||| | | |||| | || | | | | ||| | | ||| | | ||||| || || ||||| ||| |||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| ||| || || || ||||||||||| |
gttgaaaagcgaagaactgtgaagagcacactttgtaatgagagaagttcacggagccattgcgtggtttgttgcattcagccaccagcactgt-cagcattcatttttaaaaaatcaagctttttcacactatgctttgcatctatagATTATCCTGGATGTCCCAGCTGTGGGAGGAAGGTTGATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCAGCAGGTCAAACGGGATTTGAAGCCA
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G029134_T01 (Zea mays), 3'ss of exon 1
gtaagaacgatcttcttgattgatgtgtatgcatagctttatgcagcttatctctgttttaact----tactagtgtggtt--gtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
| | | ||| | | ||| |||| | | | || | | || ||| | | ||| ||| | | ||||| || || ||||| ||| |||| || |||||||| |||||||| ||||||||||| |||||||| ||||| || || || || ||||||||||| |
---------gtttgttgcattcaacc--aaccatcactttgaac-gttcattttttttaaaaccaagatttttacaaggtatactttgcatctatagATTATCCTGGATGTCCCATCTGTGGGAGGAAGATTAATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCTGCAGGACAAACAGGATTTGAAGCCA
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G062084_T01 (Zea mays), 3'ss of exon 2
gtaagaacgatcttcttgattgatgtgtatgcatagctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
| | | ||| | ||| | || | | | ||| | | ||| | | ||||| || || ||||| ||| |||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| ||| || || || ||||||||||| |
---------gtttgttgcattcagccaccagcactgtcagcattcatttttaaaaaatcaagctttttcacactatgctttgcatctatagATTATCCTGGATGTCCCAGCTGTGGGAGGAAGGTTGATGCTTGTGGACATGGCTGGATCTGAAAACATAGAAGCAGCAGGTCAAACGGGATTTGAAGCCA
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G32610.1 (Glycine max), 3'ss of exon 3
gtaagaacgatcttcttgattgatgtgtatgcatagctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
||| | | | ||| |||| | || || | ||| || | | | ||||| | || || | | | | || | || |||||||| |||||||| || || | | |||||||| |||||||| || || |||||||| || |||||||| || ||||||||||| || |
gtatg--tggtagctttggaggatggttctgattaaatctataaagttcccttgattggtaactgatta-catgtattctattctgatcagGTAATCCTTGATGTCCCAACTGTGGGAGGGCGGCTAATGCTTGTGGACATGGCAGGATCAGAAAATATTGAACAAGCTGGTCAAACTGGATTTGAGGCCA
upper sequence: AT4G14330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01350.t01 (Vitis vinifera), 3'ss of exon 2
gtaagaacgatcttcttgattgatgtg--tatgcatagctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
|| ||| |||| || || | |||| | |||| | ||| | || | | |||||| | | || ||| ||| ||||| || |||||||| || ||||| || ||||| ||||||||||||||||||||||||||||||||||| || |||||||| || |||||||| ||||| |
gtctgaatc-tcttaaaactttattaggttatgacaacctttccaaatcttcttgctttataaacttaatcttctg--tgtgcatttgcatagATAATCCTTGATGTCCCTACTGTGGGAGGAAGGTTGATGCTTGTTGACATGGCTGGTTCTGAAAATATTGAGCAAGCTGGTCAAACTGGATTGGAAGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
aacttac putative branch site (score: 2)
ttgtttctttttgt putative PPT
ttttaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacgatcttcttgattgatgtgtatgcatagctttatgcagcttatctctgttttaacttactagtgtggttgtttctttttgtagATCATACTTGATGTGCCAACTGTTGGGGGAAGATTGATGCTTGTTGACATGGCTGGTTCTGAAAATATAGACCAAGCTGGGCAGACTGGATTTGAAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC