Sequence
atgc intronic sequence ATGC exonic sequenceAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaacaagcttgatacttgatgctttagacaaaaacttatctaagatgtataaagaagctacactgttttgattttcgggtttag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36960.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36960.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 12
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaacaagc--ttgatacttgatgctttagacaaaaacttatctaagatgtataaagaagctacactgttttgattttcgggtttag---------------------------------
|| |||||||||||| |||||||||| ||||| ||||||||||| | ||||| |||||||| ||||| || ||| ||||||||| ||||| ||||||| | | | | ||||| | | | | || || | | | || | || ||| ||| ||
TAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGACATGAGgtaaggctgttggtgtctccttgtctctgcttcccatgcctccaaagccaaagtg---acaatgtcaaccttagcttttctttggggaaaagaaaaacactaatcataccattccaatgtttcag
upper sequence: AT4G36960.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA01G39330.1 (Glycine max), 5'ss of exon 12
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaac--aagcttgatacttgatgctttagacaaaaacttatctaagatgtataaagaagcta------cactgttttgattttcgggtttag--
||||||| || ||||||||||||||||||||||| ||||||||| ||||||| |||||||| || | ||||| |||||||| || |||||||| ||||| | | || ||| | || | ||| || | | | ||||| || || | || || || | ||||
TAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgatttaaatttgctgctaacttttttttactaccctactttcatcgattataagttttctgtttgtccatttttctgtaattaagatttaaat
upper sequence: AT4G36960.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA11G05940.1 (Glycine max), 5'ss of exon 12
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaa--aaaaacaagcttgatacttgatgctttagacaa---aaacttatctaagatgtataaa-gaagctacactgttttgattttcgggtttag----
|||||| || ||||||||||||||||||||||| ||||||||| |||||| |||||||| || | ||||| |||||||| || |||||||| |||| | || ||| | | || ||| | | | ||||| || | | | || | || || || ||||
TAAGAGAGCAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGCAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCCGgtactttgatttaaatttgctgccaactgtttttactaccctactttcatctattataagtttctgtttgtccatttttctgtaattgaaatttaaatgt
upper sequence: AT4G36960.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv07s0031g00600.t01 (Vitis vinifera), 5'ss of exon 12
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaac--aagcttgatacttgat---gctttagacaaaaacttatctaagatgtataaagaagctacactgttttgattttcgggtttag------
||||||||||| ||||| || ||||| ||||| |||||||||||| ||||||| || ||||||||| | ||||| |||||||| || || ||||| ||||| ||| |||||| || | | | |||| | | | ||||| |||| | | || || | | | |||| | ||
TAAGAGAAGTGGCCATAGGGGCTTTGGTTTTGTAACCTTTGCTGAAGATGGTGTAGCTGATCGTGTATCTCGAAGGTCTCATGAGATTTGCGGACAGCAGgtatggaaatggaagcttaatggtcatttttgttttacctacataattatcatagatct-tgaaagttataaagtttggtgatgtctatgtcactgatataMapped 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|86084158|gb|DR379917.1|DR379917EST: GTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAG GTAGCAATAGATTCAGCAACGCCTCTTGATGAAGCTGGACCTAGCS-TGGC
genomic: GTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaac ... tcgggtttagGTAGCAATAGATTCAGCAACGCCTCTTGATGAAGCTGGACCTAGCGCTGGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaacaagcttgatacttgatgctttagacaaaaacttatctaagatgtataaagaagctacactgttttgattttcgggtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA