Sequence
atgc intronic sequence ATGC exonic sequence...actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03120.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 1
-----actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
|||| |||| | |||||| | ||| | | || | | ||| || ||| | | |||| || || || | | | |||| || ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||| | ||||||||||| ||||| |
tgttcgttaatacttgtgtttcttattctcatcatccatcttctaatcattg-attctt--gatctatgcacgagtttcc-gtacttacatttgttgggt-ttagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG
upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 1
--actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
| ||| || | | || | | || | || | | || || || || ||| || | || | | ||| ||| |||| || ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||| | ||||||||||| ||||| |
ttgtttttcttagtctcatcatccatcttctaaccatagatccttgatctttgcatgagtttccgtacttactttttttttttacatttgttgggat--tagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG
upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 2
actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatac-atttttcagatttggtgattttt--ttcttgtgtttt-ttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
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--------------------gtaactttctgcttgat-tgttaaatgttaatttttacactcaattattattaattttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG
upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
|| ||||| || | | | | | | | | |||| | | ||| || | || ||| | || ||||| || ||||| ||||| ||||| |||||||||||||| ||||| |||||| | ||||| ||||||||| | || || ||||| ||||| |
-------------gta-actttctgcttgcttgttaaacgttaattttttacactcaatttattattaactttattat-ttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 1
-----actaatctatgtg-gtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
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tattcttgagtttatgcctgtattcttaatatttattcatgatttctc---tatgtccttcgagctta---ttttcttatttaaattattaattgagttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTGMapped 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|19876194|gb|AU237025.1|AU237025EST: AAACTTTTCGCAAGCTTTTCGATACCTTCTTCGGCAACCAGGAGATGAGG GTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAG
genomic: AAACTTTTCGCAAGCTTTTCGATACCTTCTTCGGCAACCAGGAGATGAGGgtactctcct ... gagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
atttttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaatctatgtggtgtggtttctcactgtgcatgatatgatgaatacatttttcagatttggtgatttttttcttgtgttttttgttttgagatgccagGTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
actaatc
- - - - - - ggtgtgg
- - - - - - - - - - - ctcactg
- - - - - - - - - - - - - - - - - - - - - gaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gatttgg