Sequence
atgc intronic sequence ATGC exonic sequenceTCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30450.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 5'ss of exon 12
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatga---aat----tttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
|| || || || || || || ||||||||||| ||||||||||| || ||||||| ||| |||||||| | || ||||||| || | ||||| | ||||||| || || ||||| | || | | || | | | | | |||| | | ||| || || ||| |||| | || | ||||| |
TCATGCTTTCTCCTTGACCTCCTTGATGCTCCTAGTTGGCGTCCTCGTTGGAAATTTCACCATTGGAGTTTATCACTTGTTGGTGCATTGCTTTGTGTTGgtatgactatatactattacaaattcattttgacacaatggcatgcatcatgagc---tgtaatgctttctta-ggacatt---attttgatta----aagacttctgaca--------------------------------------------------------------------------
upper sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G113276_T01 (Zea mays), 5'ss of exon 6
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactac-cacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
|| || || ||||| ||||| ||||||||||| |||||||| || | ||||||| ||| |||||||||||||| ||||||| || | | || | |||||| || |||||| | | || || | | | || | | | || | |||| || | ||| || | | |
TCATGCTTTCTGCTTGATCTCCTTGATGCTCCTAGTTGGCGCCCCAGATGGAAATTTCACCATTGGAGCCTTTCACTTGTTGGGGCATTGTTCTGTGTTGgtatgg---ttcttaatactttt------accattttattttgttttatcac--aatcttcagcatgaacagttgatacttgagttaggtccttggtttgagactttgtcc--------------------------------------------------------------------
upper sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA15G22520.1 (Glycine max), 5'ss of exon 10
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
|| || ||||| ||||||||||| ||||| || ||||||||||| |||||||||| ||| |||||||| || ||| |||| ||||| | |||||||||||||||| | | | || | | |||| | || | | ||| | || || | | | | || ||| || | |||||| || | |||
TCCTGCTTCCTTCTCGATCTTCTAGATGCCCCTAGTTGGCGTCCTCGGTGGAAATTTCACCATTGGAGTCTGTCCCTTGTGGGAGCATTACTTTGCATAGgtatgctgtctccctatgtttttt-------tttcttccattgttt-cttattatattcagtcttttgacatctttg---tgatttag-atttggcttgttcttctgtctgc------------------------------------------------------------------
upper sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 5'ss of exon 11
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
||||| ||||| || |||||||| |||||||| |||||||||||||| ||||||| ||| || |||||||| || || ||||||| ||||| ||||||||| ||| || |||| | | | ||| | | | | ||| || ||| || | | | ||| | || | || || ||| | | |
TCTTGCTTCCTTCTGGATCTTCTAGATGCTCCCAGTTGGCGTCCACGATGGAAATTTCACCACTGGAGCCTCTCTCTTCTTGGAGCAGTTCTTTGTATAGgtatgg---ttt---attctcat----------tttattccattgca-----gggatttatttcttgggaa-----gagtgggaatacaatcggggcaatcattacaactgttttttagtggatac----------------------------------------------------
upper sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ21598 (Selaginella moellendorffii), 5'ss of exon 9
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
|| ||| | ||||||| | |||||||||||||| |||||||| |||||||||| |||||| |||||| |||| | | || || | | |||||||||| | |||| | | | || | || | || | |||| | | | | | ||
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactttt--accaattactg--aagttacctgtaacagtgtttatcttgattacag---------------------------------------------------------------------------------------------------------------------
upper sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ23975 (Selaginella moellendorffii), 5'ss of exon 9
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
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TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactttt--accaattactg--aagttacctgtaacagtgtttatctggattacag---------------------------------------------------------------------------------------------------------------------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|47829383|gb|CK119067.1|CK119067EST: GAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAG TGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTG
genomic: GAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaatt ... attcttgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG