Sequence
atgc intronic sequence ATGC exonic sequenceCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17720.2 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtca-ttgctgtacttttctgtcttgtataaggaataaactaatgaccaatttat-tatacttaatctccggtgaaccag
||||| ||| ||||||||||||| ||||| |||||||| |||||||| |||| || || ||||||||| | |||||||| ||||||||||||| |||||| | || ||| || ||||| || |||| | | | | ||||||| | || || ||| || | || |
CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAGgtg---ttgcttttgctcatctcagttatggtactgctcggtctccttcatg---tgaactaattgttagttgatgtatgctc--tttcag---------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttc-tggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag--
|| || ||||||||||||||||| || || ||||| |||||||| |||||||||||||| |||||| | | || ||||| || |||||||||| | ||||||| || | | | | | || || ||| | | | | || | | | ||| | | | |||
CTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAGgt--atctgcttgttctcattatgagttaccaatgccgctaactattattttatttggaactactatatgttaactctccttgtggtgccttcaactgcag
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgta-taaggaataaactaatgaccaatttattatactta-atctccggtgaaccag
|||| ||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||| | || ||||| ||||| || ||| || | | || || || | ||| | | | || || | || ||| | | | | |||| || |||| || |
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgta---ttaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatca--tgtctgctgacaccttatttttgcatctgtattgcag---
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtca-ttgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
|||| ||| |||||||||||||||| || ||||| |||||||||||||||| ||||| |||||||| || |||||||| ||||| ||||||| | || | | || ||| ||| ||| | | || | | | | ||| | | | |||| | || | |
TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctgatat---tcttgttcagttgtaatacggcttggcctcattgacagga---actgactagctatttgtcatcttcag---------------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttg-tcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
|||| ||| |||||||||||||||| || || || |||||||||||||||| ||||| |||||||| || |||||||| ||||| ||||||| | || || || || || | ||| || || | ||||| ||||| | ||| | || | |
TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAGgtagtctcatatgctcgtccagttgtaatacagcttggctccatt--aacaggaactaactag----ctgtttgtgatcttcag---------------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G452572_T01 (Zea mays), 5'ss of exon 1
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
| ||||||||||| || || || |||||||||||||||| ||||| |||||||| || |||| ||| ||||| ||||||| | || || ||| ||| | | | | | | ||||| | | ||| | || | |
---------ACACGCGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGAAACTGGTTCCTACAGgtagtctcatatgctaatcca--gttgtaatacagcttggctccattaacagga---actaactagctgtttgtgatcttcag---------------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
|| |||||| |||||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||| | ||||||| ||||||||||||| || | | || || | | || || || | | | | || | ||| || |||| | | |
CTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAGgtc--tctgatacaaacttaatccgtggttcagttgtc-gttggaattgtttatcctgcatcttacgattttgtttcactttttgacag---------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
|| || ||| ||||||||||||| || ||||| ||||| || || |||||||| ||||| ||||||||| | |||||||| ||||||||||||| || | | || | | | | | || | | | | || | ||| || |||| | | |
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtc--tctgatacaaacttaatctgcggttcaatcgcc-gttggaattgtttatcctgcatcttacgattttgtttcacttgttgacag---------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
|| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | || |||| ||||||||||||| | | | || | | ||||||| | | || | || | || | ||| || | || || | |
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAGgtatggatacaaactta------atctatctgtggttctgtcattcttgag---tctgcttcttactattttgtttcatttgataccag---------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
|| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | || |||| || |||||||||| | | || | || | ||| || | | | | || | | || | ||| || | || || | |
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgt--atgggattaaaacttaatctata-tgtggttctgttattctt-----gagcctgcatcttactattttgtttcatttgattccag---------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgct---tgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
| || ||| ||||||||||||| || ||||||||||||||||| |||||||||||||| |||||| || | ||||| |||||||||||||||| || | | | | | || ||| | || | | || | || || |||| |||| || | ||| | |
TTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAGgtccgttttttaaattttctttatccaccattgt-ttcttgaaccctctaccatgagta--ctaacataaaattgatg-----tgatcccag---------
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtc--attgctgtacttttctgtcttgtataaggaataaactaatgacca-atttattatacttaatctc-cggtgaaccag--------------------------------------------------
|| | |||| |||| ||||||||||| || || || || |||||||||||||| ||||||||||| || | ||||| || ||||| ||||||| || | | || || | | | | || | | | | | | ||||| | || || | | | | || | || | |
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgt-attgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 5'ss of exon 11
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttt-tctgtcttgtataaggaataaactaatgaccaatttat---tatactta-atctccggtgaaccag-----------------------------------------------------
|| || ||||| ||||| || || || ||||| ||||| |||||||||||| | ||||||||||| || | |||||||| ||||| ||||||| | | || | ||| | | || | ||| |||| | | | | ||| | || || | || || || ||| | ||
CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAGgt-acgtcattgctcagccacatattttggcatcttataagtcctgta-atgaagcatgtgaatcaggaacttgtatctaaacatatgtcttcttagatttttgttagtactcttccaagtgtggtaccgaattgaattattcttctttgtcacagMapped 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|301502468|gb|HO208008.1|HO208008EST: GAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG CAATCTATTCCGCGTATTTGGAGCGTCTCAAGGAAGTACT
genomic: GAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgc ... ggtgaaccagCAATCTATTCCGCGTATTTGGAGCGTCTCAAGGAAGTACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgtataaggaataaactaatgaccaatttattatacttaatctccggtgaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA