Sequence
atgc intronic sequence ATGC exonic sequencegtagttttctcgagacctttggttgtcttttttaatcaagttttcttctggtgaagtatatgctaaactcttggaattttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 2
-----gtagttttctcgagacctttggttgtcttttttaatcaagttttc---ttctggtgaagtatatgctaaac----tcttggaattttgtga--agGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
||| ||| | ||| | || | || | ||| || ||| | | || | || | || || | |||| ||| |||| || || | || |||| || || ||||||||| | | ||||||||| ||||||||||| || || ||||||||| | |||||||||| | || |
cctcaatagatttttaatgacgaataattataaacaggaaatatgttatctcgttcatgcctaataatttctttatggtatcctgtatttttatgaacagGAGATAGCAAGTTACTTGGGGCTAGAACTTGGGAAGATAACCATAAAGAGGTTTGCTGATGGTGAAATATATGTTCAGTTGCAAGAAAGTGTACGGGGCT
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
----------gtagttttctcgagacctttggt-tgtcttttttaatcaagttttcttctggtgaagtatatg----ctaaactcttggaattttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
|| | | | |||| | | ||| || | ||||| || || ||| | | || | | | || |||| ||||||||||| |||| ||||| ||||| ||||| ||| || ||| ||| ||||||||||||| || |||||||| ||| | |||| |||||||||||||
gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatt-tgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
-----------gtagttttctcgagacctttggt-tgtcttttttaatcaagttttcttctggtgaagtatatgctaaactcttggaat--tttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
| || | | | || | | | ||| || | ||||| || | | | | | | | | ||| |||| ||||||||||| |||| ||||| ||||| || || ||| || ||| ||| ||||||||||||| || || ||||| ||| | |||| |||||||||||||
tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
upper sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
--gtagttttctcgagacctttggttgtcttttttaatcaagttttcttctggt-------gaagtatatgctaaactctt----ggaattt--tgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
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ccttcttcttctttataa-tttggttctttttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGTMapped 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|125288184|gb|EL302269.1|EL302269EST: ACTAAGCTCAAGTTGTTCTTCTTGGTACTGCTAATCCAGCTTTATCTCAG GAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCA
genomic: ACTAAGCTCAAGTTGTTC-TC-TGGTACTGCTAATCCAGCTTTATCTCAGgtagttttct ... ttttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatcaagttttcttctggtgaagtatatgctaaactcttggaattttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
tgctaaa putative branch site (score: 2)
aagtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttttctcgagacctttggttgtcttttttaatcaagttttcttctggtgaagtatatgctaaactcttggaattttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA