Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36860.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 8
-------gtaaaacctctatatcttattg-atactatg---tttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgc-tgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
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gtaaatgttaatgctttcaactttcattctatgttttgccttttatttctattatttacatcataccccttccattgttctaattttgcattgcttttgaatgtagGGTCATCATCACTTACCTGAAACCAGAGGACTTTGCTTGTCCGAAGAGCAAACTGTTCCCACT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G38640.3 (Glycine max), 3'ss of exon 5
--------------gtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatct---aattttgc-tgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
|| ||| | || | ||| || || || || | | | ||| | || | ||| ||| | | | ||| || |||| ||||| || ||||||||||||||||| || || ||||| ||||| ||||||||||||||
gtaagtgtcaatgtgtttaactttc-catttcattcatggaatattgttatttctgttctttctagtatcttgacttcgaaatgttcttttatttctcactattgaatgtagGGTCATCACCACTTACCTGAAACTAGAGGGCTATGCTTGTCAGAAGAGCAAACTGTCACCACC
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 8
-------gtaaaacctctatatcttattgat--actatgtttatactctctctttctctc-tcgc-tcatttgtttcaacctacttctatctaattttgc-tgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
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gtaagtgttaatgttttcaacttccattcttgaattttgccttttatttctcttctttacatcatatcccttctattgttctaattatgcattgctttgaatgtagGGTCATCACCACTTACCTGAAACGAGAGGACTTTGCTTGTCTGAAGAGCAAACTATTCCCACT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 4
--------------gtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgc-tgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
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gtaagtgttaatgtgtttaacttcc-catttcattcatggaatgctgttatttctattctttctagtgtcctgtcgaaatgttcttttatttctcactattgaatgtagGGTCATCACCACTTACCCGAAACTAGAGGACTATGCTTGTCAGAAGAGCAAACTGTCACCACT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 7
-------gtaaaacctctatatcttattg-atactatg---tttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgc-tgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
||| | | | | ||| || | || ||||| ||||| || | | || || | | || | ||||| || |||| |||||||| ||||||||||| ||||||||||| ||||| ||||| |||| ||| ||||
gtaaatgttaatgttttcaactttcattctatgttttgccttttatttctcttctttacatcataccccttccattgttctaattttgcattgcttttgaatgtagGGTCATCATCACTTACCTGAAACCAGAGGACTTTGCTTGTCCGAAGAGCAAAATGTTCCCACT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 9
---------------gtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgct--catttgtttcaacctacttctatctaattttgctgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
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gtaagggctaatgcattgaagtgatcatttttcat-agcaacaggtactttcttgtcttttattttaagcttccatcaagtttgaatg--ttctctttattttatgggcagGGACATCATCACTTGCCTGAGACTAGAGGACTCTGCCTGTCCGAAGAACAGACTGTTAGCACTMapped 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|86086879|gb|DR382638.1|DR382638EST: TTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACAC GGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAA
genomic: TTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctc ... tttgctgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
atctaat putative branch site (score: 3)
ttttgct CT-rich tract
ttctatctaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC