Sequence
atgc intronic sequence ATGC exonic sequence...actgaatcttgttttttcattttattaggacttattcaatacccatttgtcattgtacattgttaattttcttctgagggtgtgatactcttaatggcagGGAGCTTTATAGTAATAACATAACCGGGCCGGTTCCAAGCGATCTTGGGAATCTGACAAACTTAGTGAGCTTGGATCTTTACTTGAACAGCTTCACTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G34210.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G34210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g07760.1 (Oryza sativa), 3'ss of exon 3
---actgaatcttgttttttcattttattaggacttattcaa--tacccatttgtcattgtacattgttaattttcttctgagggtgtgatactcttaatg--gcagGGAGCTTTATAGTAATAACATAACCGGGCCGGTTCCAAGCGATCTTGGGAATCTGACAAACTTAGTGAGCTTGGATCTTTACTTGAACAGCTTCACTGGT
| | || | | | || | | || | |||| | || | |||||| | | ||||| ||| | ||| | |||| ||| |||||||||| || ||||||||||||| ||| || | || || || ||||| || || |||||||| || || |||||| | |||||||||| ||||||||||
agaaatattcctagctagtgtgttgtgctcagatcaactcaagccaatcactgagtattgtagagtattaatgttcat-------tgttttcttctttatgatgcagGGAGCTCTACAGTAATAACATAAGCGGAACGATACCTAGTGAACTTGGAAACCTCACAAACTTGGTCAGTTTGGATTTGTACTTGAACAACTTCACTGGT
upper sequence: AT1G34210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 3
--actga--atcttgttttttcattttattaggactta--ttcaatacccatttgtcattgtaca-ttgttaattttcttctgagggtgtgatactcttaatggcagGGAGCTTTATAGTAATAACATAACCGGGCCGGTTCCAAGCGATCTTGGGAATCTGACAAACTTAGTGAGCTTGGATCTTTACTTGAACAGCTTCACTGGT
||| | | || || | | | | | | || || ||| || | || || | || | | | |||| | | | | ||| ||||||||| || |||||||| || | || | | || || || ||||||||||| |||||||| || || |||||| | |||||||||| ||||||||||
tcactaatgacctcaaccatttactgtggcatgccatagcttggttactttcttttgtttttaaaattagtcactgccttc-----atatcgtgtttttat--acagGGAGCTCTACAGTAATAATATCAGTGGCACTATACCTAGTGAACTTGGGAATCTTACAAACTTGGTCAGTTTGGATTTGTACTTGAACAACTTCACTGGT
upper sequence: AT1G34210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 3
-----actgaatcttgttttttcattttattaggacttattcaatacccatttgtcattgtacattgttaattttcttctgagggtgtgatactcttaatggcagGGAGCTTTATAGTAATAACATAACCGGGCCGGTTCCAAGCGATCTTGGGAATCTGACAAACTTAGTGAGCTTGGATCTTTACTTGAACAGCTTCACTGGT
||||| || | || | | || || | | | | |||| | | | | | |||| | | | | ||| |||||| ||||||||||| ||||||| || | |||| || ||||||||||||||||||| ||| |||||||||||||| ||||||||||| |||||||||
ctttctctgaag--tggtgttctgtgcttttcatcctcaacttgtgtgctgtcaccatttttttatttgcacaagttattgag---atcaatttgattatgacagGGAACTTTATAGTAACAACATAAGTGGACAAATTCCTAGTGATCTTGGGAATCTGACAAGCTTGGTGAGCTTGGATCTCTACTTGAACAGGTTCACTGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtcattgtacattgttaattttcttctgagggtgtgatactcttaatggcagGGAGCTTTATAGTAATAACATAACCGGGCCGGTTCCAAGCGATCTTGGGAATCTGACAAACTTAGTGAGCTTGGATCTTTACTTGAACAGCTTCACTGGT
tcttaat putative branch site (score: 3)
tactctt CT-rich tract
tacattgttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgaatcttgttttttcattttattaggacttattcaatacccatttgtcattgtacattgttaattttcttctgagggtgtgatactcttaatggcagGGAGCTTTATAGTAATAACATAACCGGGCCGGTTCCAAGCGATCTTGGGAATCTGACAAACTTAGTGAGCTTGGATCTTTACTTGAACAGCTTCACTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
-ctgaatc
- - - - - - - - - - - - - - - - - - caatacc