Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 8
------------------------------------gtttgttttgttttgtatagtttcctgcaattgt------atacgacggcgcttgttttgcttataaaacgt-gttcctatcctttttc----tagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
| ||| | | | | ||| || ||||| | || | || | | || | |||| | ||||| || |||| ||||| ||||| || |||||| ||||||| ||||| || |||||||||||||| ||||| | ||||| || || || ||| |||||||||||||||
gtgctattaaccgtctttgctttttttgaatgatctaatactttggacatcaacattttgttggcattgttatgttgtttgagaattatcacttcagtaccatcactttgttcatttccttactcaaaccagCCGAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTC
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 9
----------------------------------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
| ||||| | |||| |||| || ||| |||| | | ||||| || ||| | | | ||||||||||||||||||| || |||||||| ||||| || ||||||||||||||||| || ||| | ||||| || || || |||||||| || |||||||
gttctacttatcatttagcatttcaatgaacatcagtagtttttgctggtattgttttg-acatttgaatacaagtatttcagcattgctaat----ttcattctctacttcaaaccagCCAAGTCCGTTTTTTACGGAACAACTGACGGCTTTCGAAGTGTGGCTTGATCATGGCTCCGAGGACAAGAAACCTCCTGAACAGTTACCCATAGTTCTTC
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcc-----tttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
||| | | | | | | | ||| | | || | | || | ||| | | | |||| | ||||| |||||||||| || || |||||||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| ||||| |||||||| || ||||||||||
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctggttt-tatcatctcatatgcccag-ttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgct--tataaaacgtgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
|||||||| | | || ||| | ||| || | | || | | | | || | || || | ||| || |||| ||||| ||||| || |||||| ||||||| ||||| |||||| | || ||||| ||||||| ||||||||||| |||||| | ||||| ||||| |
tgttgtcttgatgtttctttgtttttatccatgtaattttttt---ttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 3'ss of exon 9
--gtttgtttt---gttttgtatagtttcctgcaattgtatacgacggcgcttgt------tttgcttataaaacgtg-ttcctatcctttttct---agCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
|| ||||| ||| |||| | ||| | | | || || |||| | || || || || || ||||| | | |||| ||||| ||||| || |||||| |||||||||| ||||||||||| || ||||| ||||| ||||||||||| ||||| | ||||| |||||||
tttttcgtttttaaaatttttatatcatttaattattatttgtgtcgaaatcagtagcaaatttgaaaacaagacttgatttttagcctttctattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTC
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S88_199V6.1 (Physcomitrella patens), 3'ss of exon 9
--------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgt--------tttgcttataaaacg-tgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
||| || | || ||| |||| | | | | | || || |||| | || |||| | || || |||||||||| |||||||| || || ||||||||||| ||||||||| | || ||||| || || |||||||||||||| || | || || ||||| |
atgttacggttaattctcacttctat--tttcatttagtcaagaaatgccgcctctgaacttgaaacttgcctgctgttcggtgtttgaaacccaattgcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116411083|gb|EG453675.1|EG453675EST: GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG CCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
genomic: GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttg ... ctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
EST:
gi|116411080|gb|EG453672.1|EG453672EST: GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG CCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
genomic: GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttg ... ctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
tgttcctatccttttt CT-rich tract
ttttgcttataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG