Sequence
atgc intronic sequence ATGC exonic sequencegtaagaactcaggattcaggaatatcaaacttactagccataaactactattgtttcttaatttatgttttatcttgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17210.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g57160.1 (Oryza sativa), 3'ss of exon 4
---------------------------gtaagaactcaggattcaggaatatcaaacttac--tagccat--aaact---actattgtttct-taatttatg------ttttatcttgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
| || || | || || || | |||| | | | | ||| || | ||| | ||| || || |||| || |||||| ||||| |||||||| ||||||||||||||||| |||||||||||| | ||||| ||||||||| |||| |||| ||||||| |||||
gtatgtttacttttcttccatgttctcatgtgatgtcttggttttggcattattagtttacaatgactttggagactttagctttcgttgatataacttctgatttgcttttgctttctagGCTAGGAAGCTTATAAGCCTTTGTGGATGGGAGCCTAGGTGGCTTCCAAATGTTCAAGACTGTGAAGAAAATTCAACCCACTCAGCTAAAAATGCAGATT
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g05610.2 (Oryza sativa), 3'ss of exon 4
--------gtaagaactcaggattcaggaatatcaaacttactagccata--------aactactattgtttcttaatttatgt----tttatct------tgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
| | | | | | | | | ||| || ||| || | | || ||||| || || | |||| | ||||| || || || |||||||| ||||||||||| |||||||||||||||||| | || || || |||||| |||| ||| || || | | || |
gtaaatctcttgttatttatgctctcatatctttattctttgctgctatagtcctcagaatttgtggctttatttaatctaggtcacttccatctaatttatctagGCACAGAAACTTATAAGCCTTTGTGGATGGGAACCTAGATGGCTTCCAAATGTACAGGACTGGGAAGAAAATTCAACCCGTTCTGCCAAACATACAGCCT
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G040145_T01 (Zea mays), 3'ss of exon 4
--------------------gtaagaactcaggattcaggaatatca--aacttacta--gccataaactactattg--tttcttaatttatg---ttttatc-------ttgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
||| | | || | | | ||| | ||| | | | | || |||||||| | ||||||| |||||||| |||||||| |||||||| ||||||||||||||||| |||||||||||| | ||||| ||||||||| |||| | || ||||||| |||| |
gtatgctggtcccttttcatgtacacatgctatgttttttattggcgctaacatgctattatcttgcgttgcctccagcttctttaatttaggtgcttttatcaatgagtttgtagGCACAAAAGCTCATAAGCCTGTGTGGATGGGAGCCTAGGTGGCTTCCAAATGTTCAAGACTGTGAAGAAAATTCAACGCATTCAGCTAAAAATTTACCCT
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G013114_T01 (Zea mays), 3'ss of exon 4
-------------------------------gtaagaactcaggattcaggaatatcaaacttactagccataaactactattgtttct---taatttatgttttatct-tgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
| | |||| || | | || | ||| | |||| ||| | | | | | || | ||||| || ||||| || ||| | |||||||||||||||||||||||||| ||| | |||||||| ||||| |||| | | || || ||||||| ||
gtatatctcttcatctcttgccattgattccttcttgttgcctttttcattgatgtattattttcagaacatggagctttatttgatctaggtcactcccatctgattgatatagGCACAGAAGCTTATTAGCGTTTGTGGATGGGAGCCTAGATGGCTTCCTAATGTTCAAGATTGGGAAGAGAATTCGACACGCTCTGCCAGAAATGCAGGCT
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G18570.1 (Glycine max), 3'ss of exon 4
---------gtaagaactca--ggattcaggaatatcaaactta--ctagccataaactactattgtttc-----tta-atttatgttttatcttg-tagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
||| | | | || || | ||| | | ||| | | |||| |||| ||| ||| || || | | |||||||||||||| ||||| || |||||||||||||| | |||||||| || | | || ||||||||||| || || |||| |||| |||||| | |
tgttttatcttaattatttatcacatgcaagtgtatttttgccaatttggccttttggttttattatttccattcttacattaattttccacttcaatagGCTCAAAAGCTCATAAGTCTTTGTGGATGGGAGCCACGGTGGCTTCCGAACGTGCTTGACTGTGAAGAACAGTCAGCTGAATCTGCTAAAAATGGTTACA
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G40380.1 (Glycine max), 3'ss of exon 4
------------------------------gtaagaactca--ggattcaggaatatcaaactta--ctagccataaactactattgtttc-----ttaatttatgttttatctt--gtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
||| | | | || | | ||| || | ||| | | |||| |||| ||| ||| ||| ||| |||||||||||||| ||||| || |||||||||||||| | |||||||| ||| | | || ||||||||||| || || |||| |||| |||||| | |
gtaagattttttttgatatgttgttttatcttaattatttatcacatataagtgtatttttgctaatttggccttttggttttattatttccattcttacgttaattttccacttcaatagGCTCAAAAGCTCATAAGTCTTTGTGGATGGGAGCCACGGTGGCTTCCGAATGTGCTTGACTGTGAAGAACAGTCAGCTGAATCTGCTAAAAATGGTTACA
upper sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtaagaactcaggattcaggaatatcaa--acttactagccataaactactattgtttcttaatttatgt-tttatctt--gtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
| ||| ||| ||| | || ||| | | || | ||| | || |||||| | | | ||| |||| | |||| || || || |||||||| |||||||||||||| ||||||||||||||| | ||||| || ||||| |||||||| ||||||||||||||||| ||
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctat-tcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTTMapped 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|116473267|gb|EG515859.1|EG515859EST: TATCAGCTGCAGAAACGTACAAAGAAGAGGCTTTCAGTAATTACTCTCGC GCTCAAAAGCTGATAAGCCTATG
genomic: TATCAGCTGCAGAAACGTACAAAGAAGAGGCTTTCAGTAATTACTCTCGCgtaagaactc ... tatcttgtagGCTCAAAAGCTGATAAGCCTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaacttactagccataaactactattgtttcttaatttatgttttatcttgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
ttttatctt CT-rich tract
ataaactactattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaactcaggattcaggaatatcaaacttactagccataaactactattgtttcttaatttatgttttatcttgtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT