Sequence
atgc intronic sequence ATGC exonic sequenceATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G15080.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g49820.1 (Oryza sativa), 5'ss of exon 6
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag--------------------------------
||| | ||| | ||||| || ||||||| ||||||| ||| || | || ||||||||||||||||| ||||||||||| || || | || | ||| ||| |||| | | || | ||| | | || | || |||| | | || |||| | | | || ||| |
ATTATTATTCTCCCTCTGCTCCTTGCAGCCTTGGTTGCTGTTTCTCGGGTAGATGACTATTGGCATCATTGGCAAGATGTGTTCACCGGTGGAATTTTGGgtaggttaatttt-atagtgttacctttgcagatt--atacctcgcaacaagtaaaggaggt-actgacaagtgtgctgcatgtaattcttggaaggttctaactttactgttaaaactttgcag
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttt---tgtcttttttaactcatgaattcaaaattacgtgagaaacaaa-gctgatgacagacacacatctttcttgcaatgtccag
| || || | |||||||| || || || | || | ||| || |||||||||| || |||||||||||||||||||| |||| || | |||||||||||| | || || || |||| | | | | ||| || | | | || |||| | || | || ||| | | | | |||
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G077187_T01 (Zea mays), 5'ss of exon 6
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag---------------------------------------------------------------
||||| ||| ||||| || ||||||| || || | || || |||||||||||||||||||||| |||||||| || | | || | | | ||| || | | ||| | || | | | || || | | | | || || ||||| | | |
ATTGTCCTTTCCCCTCTGCTTCTTGCAGCCTTAGTGGCAGTTTCTCGAGTTGATGACTATTGGCATCATTGGCAAGACGTATGTACTGGCGGATTACTTGgtaggtcttgaataacacaccccctctcgttccctccacagacactacaaagaaatggaaacgttatgttcatatggttcttctattctatgaaatgtatgtacatagtacatacgattctcaaaagttgaaggtatttttttttacaacgtgcag
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G18450.2 (Glycine max), 5'ss of exon 6
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtt------tgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag
||||| | || || || || || ||||| || ||| ||| || | |||||||| ||||||||||| ||||||||||||||| |||| | |||||| |||| || ||| || ||| | | || ||| || || | | || | | | | |||| ||||
ATTGTTTTCTTTCCGCTTCTTGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTTTTTACTGGAGGGCTTATAGgtctgttgaagactggattttctttgtttgatttattaatatgtaaatatacttttctccagactttttatacg-----agcttttatgcag-------
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G41580.1 (Glycine max), 5'ss of exon 6
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag
|||| | ||||| | || || ||||| || ||| ||| || | |||||||| ||||||||||| ||||||||||| |||| |||||| | ||||||| |||| | || | || | | | | ||||| | | | ||||| | ||| | | | || ||| || | |
CTTGTTTTCTTACCATTCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTAATAGgttagtttactgatgccagatt-gattaaatatttcaataaaccctttt---caaagtttctgata--cgaatattttttttaccag------
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 5'ss of exon 5
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttct-tgcaatgtccag-----------------
||||| | | || |||| ||||||| | || || || || |||| ||||||||||||||||||||||||||||| |||| |||| | | |||||| ||||| | | || | | | |||||| || || | | | | ||| | |||| | || | ||| |
ATTGTTTTCCTGCCCATACTTCTTGCAGCTCTAGTGGGAGTTTCTCGAGTAGATGACTATTGGCATCACTGGCAAGATGTATTTGCCGGAGGTGTAATAGgtctgttt-tatcagtaccgatga--ttatgaatggaatctttccttactctacttttttctgatttatacactcttctcagtataattctttgtccttcctctctggcag
upper sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ17723 (Selaginella moellendorffii), 5'ss of exon 5
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag
||||| | | || | || | |||| | |||||||| |||| | ||||||||||||||||| || |||||||| || |||| || |||||||||||| | ||| | || | | ||| || | | || || ||| | ||||
ATTGTCGTCGTCCCGTTGCTCGGTGCAACGTTGGTTGGGATATCACGCGTTGATGACTATTGGCACCATTGGCAAGACGTGTTTGCCGGGGCTATCATAGgtacactg-----tgttctacttggttttttttttct---ttctttttgtgcttaattctattacattc-cacag------------------Mapped 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|19742481|gb|AU227834.1|AU227834EST: TGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAG GATT-ACTGTGGCCACATTTTGTTATCTGCAATTTTTCCCTCCTCCATACG
genomic: TGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgt ... caatgtccagGATTGACTGTGGCCACATTTTGTTATCTGCAATTTTTCCCTCCTCCATACG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttttgtcttttttaactcatgaattcaaaattacgtgagaaacaaagctgatgacagacacacatctttcttgcaatgtccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT