Sequence
atgc intronic sequence ATGC exonic sequence...cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttcgaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G32660.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
cgtgtatagtgtttgtgtagtttgtttactcatgtggatttttt--cgaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
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tgcttataaaacagttgtcgttc-tttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttct-tcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
cgtgtatagtgt--ttgtgtagtttgtttactcatgtggattttttcgaa--gtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
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--ttgacagtaaaatcattttgttc-ttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttat-tcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 4
cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttcgaa--gtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
| |||| | | | | ||| || ||| || | || || | || || |||| | ||| | | |||| | |||| | | ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| |||| | || ||| ||| ||||| ||||| |||||| | || || |
cctgtagtatagtctttttgttc-ttcgctcgtgaaggttccctcatatggtcacaaattaaaaatattctttat-tcaatggatatcaatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 4
cgtgtatagtgtttgtgtagtttgtttactcatgtggatttttt---cgaagtttggaactaaac-ggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
||||||| | | | | | | ||||||| |||| | | | || |||||| | | ||| ||||| | |||| | | |||||||| || ||||| || ||||||||||| ||||| || ||||| |||||||||||||||||||||| | |||| ||| ||| ||||||||||| |||||| | |||||||
----tatagtggattgtttttatatatgtccatgtgggttttattcatggatttgataactaagcagaaacattcctttcaatgcattttaatggtgttatcagGTCTTTGAGAAGCTTGGACCAAGCTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTCCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT
upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 5
cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttc---gaagtttggaactaaac---ggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
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----tgtgatagtt-tg-aattaatttctccctgtggacttcattcataagactggaaacttaacattgaaatcttcctttgaatgcactttaatggtgttaccagGTGTTTGAGAAGCTTGGACCAAGTTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTTCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTTMapped 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|163990545|gb|ES114651.1|ES114651EST: CTGTGTACAGATGAAGAACTGGTTTGATTACCGAAATCATATTTGCATT GTGTTCGAGAAGCTTGGGCCAAGTTTGTT
genomic: CTGTGTACAGATGAAGAACTGGTTTGATTACCGAAATCATATTTGCATTgtaagtatcc ... gtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
aactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttcgaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
- - - - -tgtttgt
- - - - - - - - - agtttgt
- - - - - - - - - - - - - - - - - - - - - - - -agtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actctaa