Sequence
atgc intronic sequence ATGC exonic sequence...aaacacatgcataaagcgaatacatataaagaagatacatagtagaaaactagatataattctaaatagttttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73805.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73805.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G04920.1 (Glycine max), 3'ss of exon 3
aaacacatgcataaagcgaatacatataaagaagatacatagtagaaaactagatataattctaaatagttttgttttgtacaacttggggttgg---tgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
| | || | | ||| | | || || | || | | | | | |||||||| | || | || ||| || ||||||||||||||||||||||||||| ||| | | |||||||||||||| ||||||||||| || ||||| || || || ||||| || | |||
--atctaaa-atttggtggatatgaaagtttactattaatgttgtaatttttgttgttgtcctaaatagaatatttatatattttttgttcatgcatttgaagTGTACAAGAAACATCACCCACCTATGCTCAACGACGAAGTGTGGCGCCTAGAGAAGATTGGTAAAGACGGAGCTTTCCACAAAAAATTGTCCAAAGAGGG
upper sequence: AT1G73805.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G31450.1 (Glycine max), 3'ss of exon 3
-------aaacacatgcataaagcgaatac-atataaagaagatacatagtagaaaactagatataatt-ctaaatagttttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
|| || || | ||| || | | | | ||| || | | ||| || | ||| || | || |||| || | || | || |||||||||||| ||||| ||||| |||||| | | |||||||| ||||| |||||||||||||| |||||||| || || |||| || | || ||
acatttttgccagttgagaaaggaatttaccattgatatgtgtgatatactaaatatctatattttatttcttactaattttattct-tatacatt--------tgaagTGTACAAAAAACACCACCCTCCAATGCTTCATGACGAAGTTTGGCGCCTAGAGAAGATAGGTAAAGATGGAGCTTTCCACAGAAAATTGTCATCAGAGGG
upper sequence: AT1G73805.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G34760.1 (Glycine max), 3'ss of exon 3
aaacacatgcataaagcgaatacatat-aaagaagatacatagtagaaaactagatataattctaaatagtt--ttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
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tgacaccta---aaatttggtggatatgaaagtttattattgttgtaatttttgttgttgtcgtatatagaaaatttatatatttgttttcatacatttgaagTGTACAAGAAACATTACCCACCTAAGCTCAATGACGAAGTGTGGCGCCTAGAGAAGATTGGTAAAGACGGAGCTTTCCACAAAAAATTGTCCAAAGAGGG
upper sequence: AT1G73805.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G10440.1 (Glycine max), 3'ss of exon 2
----------aaacacatgcataaagcgaatacatataaagaagatacatagtagaaaactagatataatt-ctaaatagttttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
|| || | | || || | || || ||| || | | ||| || | ||| || || |||| |||| |||| | ||||||||||| ||||| |||| |||||| | | |||||||||||||| ||||||||||||| |||||||| || || |||| ||| | || ||
ctaacatttttgccagttgtaaggaatttatttat-cattgatattatatactaaatatctacattttatttcttcctattttttttttatacattt----------gaagTGTACAAAAAACACTACCCTCCAATGCTTCACGACGAAGTGTGGCGCTTAGAGAAGATAGGTAAAGATGGAGCTTTCCACAGGAAATTGTCATCAGAGGG
upper sequence: AT1G73805.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g03370.t01 (Vitis vinifera), 3'ss of exon 3
aaacacatgcataaagcgaata-catataaagaagatacatagtagaaaactagatataattctaaatagttttgttttg--tacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
| ||| | || | || || | | | || || ||| || || || | | ||| || | ||| |||||||| || || ||||| |||||| | || || || ||||| || |||||||| || ||||||||||| || ||||||||||| |||| |
---ggccccagtaattgaagtatcccatggagcaatcatctggtcttttcctttataagatatctgctaattactatctacttactttttcccacgtatacagTATACAAGAAGCACCATCCACCCATGTTAAACGATGAGGTATGGCGCCTTGAGAAGATCGGAAAAGATGGGGCTTTCCACAAGAAGCTGGCCTCCGAGAA
upper sequence: AT1G73805.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g03390.t01 (Vitis vinifera), 3'ss of exon 3
---aaacacatgcataaagcgaatacatataaagaagatacatagtagaaaactagatataattctaaatagttttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
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tcttagtac-ttcactaaatgcatgctttgttctcgagcttataaca--attcaatttctcaaacgaactatctggtaattatgctttttcctctttattcagTGTACAAGAAGCACTATCCACCAATGCTGGATGATGAAGTATGGCGTCTTGAGAAGATTGGAAAAGATGGGGCTTTTCACAAGAAGCTAGCCTCGATAAAMapped 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|301502025|gb|HO207565.1|HO207565EST: TTGTGAAGCGATGACTGAAGCGATTGTTGTTAGAGATCATCGTGGAGAAT TGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAG
genomic: TTGTGAAGCGATGACTGAAGCGATTGTTGTTAGAGATCATCGTGGAGAATgtaagtttat ... gttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaactagatataattctaaatagttttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
ttctaaa putative branch site (score: 2)
tagatataattctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaacacatgcataaagcgaatacatataaagaagatacatagtagaaaactagatataattctaaatagttttgttttgtacaacttggggttggtgaagTGTACAAGAAACATCACCCACCAATGTTAGAAGACGAAGTGTGGCGGCTAGAGAAGATAGGCAAAGATGGGGCCTTTCACAAGAAGCTCTCCTCTCGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
aaacaca
- - - - -cataaag
- - - - - - - - -gaataca
- - - - - - - - - - - - - -aaagaag
- - - - - - - - - - - - - - - - - - - - - - -aaaacta