Sequence
atgc intronic sequence ATGC exonic sequencegtctctcaatttgtctttaagcttgtttacataagttgattgatgctttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09900.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09900.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 9
------------------------------------------------------gtctctcaatttgtctttaagcttgt-ttacataagttgattgatgctttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG
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gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG
upper sequence: AT5G09900.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------gtctctcaatttgt-ctttaagcttgtttacataagttgattgatgctttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG
| | ||| | |||| ||| ||| | | ||| || | || || | || | |||||||| || ||||| ||||| ||||| ||||| || || || ||||||||||| |||||||| ||||| || | ||
gtaaataactgatgacattatatttcttctcaccccatcaattttgttggttgatattgtatgatatgctttatgctttatgttttatacttctttttgtgaac--attaatatcgagcattttttcctacctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG
upper sequence: AT5G09900.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------gtctctcaatttgtctttaagcttg--tttacataagttgattgatgctttaaagttattaatttattctg--cagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG
| ||||| | | ||| ||| | ||| | || ||| | | | | | |||| ||||| ||||| ||||||||||| |||||| |||||||||| |||||||||||||| ||||| || || || ||| | ||
gtagtgtttctctgtacatttagttccatacaataatttttttgatcatttgagttttgagttattgggtaattatttgtatgcaaaactgtcttcttttcagAACATCCTTGTTGTCTCAAAATACTACTCAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAGMapped 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|86083515|gb|DR379274.1|DR379274EST: GGGTGACAAAGCTGGTGAAGATCTGAAACTGAGAATCATCGAACA--T-- AATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTT
genomic: GGGTGACAAAGCTGGTGAAGATCTGAAACTGAGAATCATCGAACATGTAAgtctctcaat ... tattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagcttgtttacataagttgattgatgctttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG
tattaat putative branch site (score: 2)
tttattct CT-rich tract
attgatgctttaaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctcaatttgtctttaagcttgtttacataagttgattgatgctttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA