Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaaaaccgaagcaaaacattgtgccgtttttcaatcctagcgacttcctttaacatcactttcattcaatgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G14670.2 (Glycine max), 3'ss of exon 9
gtaagcaaaa-----ccgaagcaaaacatt---gtgccgtttttcaatcct------agcgacttcctttaa---catcactttcattcaatgaat-gcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
||||| | || | || || || | ||| ||||||| || | | || || || | | || | | | ||| |||||||| || | |||||||| |||||||| |||| || ||||| || ||||| || ||| | || || |||||||||||| | ||||||||||||||||
gtaagtataatgtatctgattcataattgttcagtgaattttttcatcccccctttgattaattttctcaaattgtgtgaacaacaattattaaattacagGTTCCACCGAGTACGCCAGTGGTTAATGCACTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTAAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G31450.3 (Glycine max), 3'ss of exon 9
-gtaagcaaaaccgaagcaaaacattgtgccgtttttcaatcctagcg--acttcctttaac---atcactttcattcaat-----gaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
| | ||||| || || |||| | | | ||| || | | ||||||| || || || |||| | | |||||||| || || || ||||| || ||||| ||||| || ||||| || ||||| || ||| | || || |||||||||||| | ||||||||||||||||
gtctaatactaccgattcataa--ttgttcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattattaaattacagGTTCCACCGGGTACACCAGTGGTGAATGCGTTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTGAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 6
gtaagcaaaaccgaagcaaaacat---tgtgccgtttttcaatcctagcgacttcc--tttaacatcactttc---attcaat-----gaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
||||| || | | | ||| ||| | | | ||| || | | || ||||| | || || |||| | | |||||||| || || || ||||| || ||||| ||||| || ||||| || ||||| || ||| | || || |||||||||||| | ||||||||||||||||
gtaagtctaatactaccgattcataattgttcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattattaaattacagGTTCCACCGGGTACACCAGTGGTGAATGCGTTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTGAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------------------------------gt-aagcaaaaccgaagcaaaacattgtgccgtttttcaatcctagcgacttccttt-------------aacatcactttca-ttcaatgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
|| ||| ||| | | | | || ||||| | || | || | | || | ||| || || |||||||||| || || || ||||| || ||||| ||||| || |||||||||||||| || ||| || | || |||||||||||| | || || ||||| ||||
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 9
--------------gtaagcaaaaccgaagca---aaacattgtgccgtttttcaatcctagcgacttcctttaacatcactttcattcaatgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
| | | | | | ||| ||| | || | | | |||| | || | | | || |||||||| || ||||| ||||| || ||||| || |||| ||||| |||||||| |||||| |||| || |||||||||||| | ||||| ||||||||||
gacatcaaagttttaccttcttgtttggaatatgcgaggaatgtagagttagttgatagcattatgatgttgtaacgttttgttggtgtattaaaaacagGTTCCACCAGGCACTCCAGTGGTGAATGCACTGGCGAAGCAGCGGGCAATGCTCGAGAACATACTAAGGGCTTGTGTTGGATTGGCTCCCGAGAACAACAMapped 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|124985942|gb|EL058499.1|EL058499EST: TTTCCTATCCGGTGGCTACTCTCCTAAGTTACCTCTCAAAGGCACCACTG GTTCCTCCTGGCACGCCAGTTGTTAATGCTTTG
genomic: TTTCC-ATCCGGTGGCTACTCTCCTAAGTTACCTCTCAAAGGCACCACTGgtaagcaaaa ... atgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgtttttcaatcctagcgacttcctttaacatcactttcattcaatgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
ctttaac putative branch site (score: 3)
tttaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaaaaccgaagcaaaacattgtgccgtttttcaatcctagcgacttcctttaacatcactttcattcaatgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT