Sequence
atgc intronic sequence ATGC exonic sequencegtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13670.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
-gtatctacacttttcatgaatacttttgaacactttcgtcattatg-gtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
|| | |||||| |||| | || || || ||| || || ||| || | | ||||| | | | || | | || | | ||| || | ||||||||||| ||||| ||||| || ||||| || || || |||||||||||||||||||||| |||||| || ||||| || |||||||
ggtcctttttcttttc-cgaatg----tagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttga------tggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 13
gtatctacactttt-catgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC-
| | | | | || | || || | | | ||| | ||| | || || || | | | | || || | || ||| ||| ||||| ||| || ||||||||||| || || ||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||| || ||||| |||||||||||
--accaagaatccaatatatgaatttctgcagatctcta-catacaagcattctgct-gttgctaactctaa----tttttggtgacttgtattctaat---ttatgcaggCACACAGTATACACAACAATCATACAAAGTAAGTGACTCATTCCCATTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTGACCTCAATGGCC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 11
-gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| | | || || | || || | | | ||| | ||| | || || || | | || | || || | || || ||| ||||| ||| || ||||||||||| || || ||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||| || ||||| || ||||||||
tttctttggaccaag-atatgaatttctgcagatctcta-catacaagcattctgct-gttgctaactctga----tttttggtgacttgtggtctaat---ttatgcagGCACACAGTATACACAACAATCATACAAAGTAAGTGACTCATTCCCATTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTGACTTCAATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
gtatctacactttt-catgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| | || || | || |||| || | ||| | | | | | | | | || || | | || || | || ||| || || ||||||||||||||| || || ||||||||||| || || || ||||| ||||| |||||||||||||| ||||||||||| || ||||| || ||||||||
-tgcttttgtttgaacacgtgggtttctgaagacctctaca--tataatgctcagcaactgtt---acctctgattt-tgttgtgatttatgatctaat---ttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| | | | || | || |||| || | ||| | || | | | | || || | | || || || || ||| || || ||||||||||||||| || || || |||||||| || || || ||||| ||||| |||||||||||||| ||||||||||| || ||||| || ||||||||
gcttttgt-ttgaacacatggatttctgaagacctctaca--tataatgcttctgcaactgtt--acctctgattt-tgttgtgatttattatctaat---ttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 13
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaat-tatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| ||| ||| |||||| || | || | | || || |||| | || | |||| || | | ||| || | || ||| | || ||| || || ||||| || |||||||||||||||||||| || || || || || |||||||||||||| ||||||||||| ||||||||||| || |||||
--accta---tttacatgaagacact-gattatgagtccccagttgctaattta-tggtagtt--attttcagcc-actttatcatttgaccataaccaaatatctgcagGCACACAATATACTCAACAGTCTTACAAAGTAAGCGACTCCTTTCCCTTTAAATGGATAAACAAGAAGTGGAGAGAAGGATTCCATGTAACTTCCATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtc-tctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| || | || |||| | ||| || | || || || || | ||||| | | || || | | ||| | || ||| || |||||||||||||| |||||||| || || || || || || |||||||| || ||||||||| ||||||||||| | || || || |||||
-----cgtcatagtcctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaac-----agGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------gtatctacact-tttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggt-tttcaaa----tgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| || | | ||| |||| | || | | | || | | |||| | || | | || ||| | || || | | ||| | | || || ||| ||| ||| || ||||||||||||||||| ||||| || || || || |||||||| || ||||||||| |||||||||| | || || ||||||||
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
| | ||| | | | || | | | ||| |||| ||| | | ||||| | ||| || | || || || || || |||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||||| || | || || || |||||
--------------------------------gtattgtcgctgt----tattgatggccactggcattgtcgctgacgc-gtgtttcccc-------------cgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
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--------------------------------gtattgtcgctgt----tattgatggccactggcattgttgctgac-----gcgtgattcccc---------cgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|86059947|gb|DR355704.1|DR355704EST: TTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG GTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCA
genomic: TTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAGgtatctacac ... aattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
ttttcaaatgaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA