Sequence
atgc intronic sequence ATGC exonic sequencegtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtattacttattggttagagtagctagtccttacctttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAACTGGATATAATCATCTTCCATTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11740.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g35710.1 (Oryza sativa), 3'ss of exon 5
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtatt-acttattggttagagtagctagtccttacc-tttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAAC-TGGATATAATCATCTTCCATTCT
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-------------------------------gtattcttttctgtaatactaatcttcaccctaaggttaaattatatgttattcactgtttgcc--tcttcctttggaaa------agTGGGGTGGCATTTCTTCTGAGGAGCATGATGAAGCTGTTATGCTTGAGGCTGCAATGTTTGGTGGAATTCCAGAAGGACCCATGTATCCGTTCTCAATGC-
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g43300.1 (Oryza sativa), 3'ss of exon 6
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtattacttattggttagagtagctagtccttacc-tttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAACTGGA-TATAATCATCTTCCATTCT
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------gtggtat---tttaatccatcacacctgtaatgagatagaatttaaccat-act-----------acagct--tcttcactgcttacaaacccgttaatttttgttgcaaagTGGGGTGGCATTTCTTCTGAAGAACATGATGAAGCTGTTATGCTTGAAGCTGCAATGTTTGGTGGAATTCCTGGAAGAGCAGCATATCCATTTTCTCTCC-
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G073504_T01 (Zea mays), 3'ss of exon 5
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtat-tacttattggttagagtagctagtccttacctttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAAC-TGGATATAATCATCTTCCATTCT
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---------------------------gtattata--taatctgtggttccaatgtgcgctaagacattagatggatttgt--ttaattt--ctgacgtcttttt----acaataaagTGGGGTGGCATTTCTTCTGAGGAACATGATGAAGCTGTTATGCTTGAGGCTGCAATGTTTGGTGGAGTTCCTGAAGGACCAACATATCCTTTCTCTATGC-
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G112839_T01 (Zea mays), 3'ss of exon 5
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtattacttattggttagagtagctagtccttacctttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAAC-TGGATATAATCATCTTCCATTCT
| | || | ||||| | ||| | ||| | ||| || || | || || | || | ||||||| |||||||| ||||||||||||||||||||||| ||||| ||||| || ||||| || || || || || || | | | ||||| |
---------------------------gtattataata----tgtggttccaatgcgcgctatgacattacacagcatttgtttaattt--ctga--cttctttctttacaataaagTGGGGTGGCATTTCTTCTGAGGAACATGATGAAGCTGTTATGCTTGAGGCTGCAATGTTCGGCGGAGTTTTTGGAAGACCAATGCATCCTTTCTCCATGC-
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G084406_T01 (Zea mays), 3'ss of exon 4
gtatccgtaaaatctgttttgtttattacactgaaaccag--actagaattccagtattacttattggttagagtagctagtccttacctttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAACTGGAT-ATAATCATCTTCCATTCT
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--------------------------------gtattcagttatcatcatgcctctactgagctatggtctg--caaattatagttccatcaactcacagtgttgttttaat-ttcaagTGGGGTGGTATTTCTTCTGAAGAGCGTGATGAAGCTCTTATGCTTGAGGCTGCAATGTTTGGTGGGATTCCTGAAGGAGCACCATATCCATTTTCCTTCC-
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G14020.1 (Glycine max), 3'ss of exon 6
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtattacttattg-gttagagtagctagtccttacct-----ttgctaatactctattgtgt-atgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAA---ACTGGATATAATCATCTTCCATTCT
||| | | || ||| | | || || || || || |||||||| || | | || ||| | || || | ||| || | | | | ||||||| |||||||| || ||||| ||||||||||| || ||||| || || || ||||||||||| ||||| ||| ||||| ||| | || | ||
------gtataggcc-ttcactttgtccttttccaaaaggattaaaactctgttattacttgccatgtcatctcaacttttccctgtctcccaattcccaatcttcactaaaatgaaattgcagTGGGGTGGCATTTCTTCAGAGGAGCATGATGAAGCAGTAATGCTTGAAGCGGCAATGTTTGGTGGAATTCCAGAAGGGACTGGGTATCACTATGGTT-ATG--
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G03480.1 (Glycine max), 3'ss of exon 6
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtattacttattg-gttagagtagctagtccttacct-----ttgctaatactctattgtgtatg-ctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAA---ACTGGATATAATCATCTTCCATTCT
||| | | || ||||| | ||| || || || || |||||||| | | | | ||| | ||| || | ||| | | || | ||||||| |||||||| || ||||| ||||||||||| || ||||| || || || ||||||||||| ||||| ||| ||||| ||| || | ||
------gtataggcc-ttcactttatccttttcaaaaaggattaaaactctgttattacttgccatgccatctcaaattttccctgcctcccaattcccaatctttactaaaataaaattgcagTGGGGTGGCATTTCTTCAGAGGAGCATGATGAAGCAGTAATGCTAGAAGCTGCAATGTTTGGTGGAATTCCAGAAGGGACTGGGTATCGCTATGGTT-ATG--
upper sequence: AT4G11740.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0025g04050.t01 (Vitis vinifera), 3'ss of exon 6
gtatccgtaaaatctgttttgtttattacac-tgaaaccagactagaa--ttccagtattacttattggttagagtagctagtccttacctttgctaatactctattgtgta--tgctct--agTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAA---CTGGATATAATCATCTTCCATTCT
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gtatctctt---ttcattacataaatcctttgtgaattctcaatgaaaatttctagctaaacctgatattta-attctcttattatggatgtgaatatgactttactcctttactgcttttaagTGGGGAGGCATCTCTTCCGAGGAACATGATGAGGCAGTCATGCTTGAGGCTGCGCTCTTTGGTGGAATTCCTGATCATTTTGGATTTGGTCCCCATCGAT---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|125029768|gb|EL102037.1|EL102037EST: GGCAGTGGGTTTCCTTCTGAG TGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCA
genomic: GGCAGTGGGTTTCCTTCTGAGgtatccgtaa ... tatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggttagagtagctagtccttacctttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAACTGGATATAATCATCTTCCATTCT
tgctaat putative branch site (score: 2)
taatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccgtaaaatctgttttgtttattacactgaaaccagactagaattccagtattacttattggttagagtagctagtccttacctttgctaatactctattgtgtatgctctagTGGGGAGGCATTTCATCTGAGGAACATGATGAAGCTGTCATGCTCGAGGCAGCCATGTTTGGTGGCATTCCTGAAACTGGATATAATCATCTTCCATTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG