Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtatttctgtcatggccattttacaattcactgcttgtttgcatatgttgttaccagacaatataatctcccgcttttttatggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01320.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 6
---gtgtgtatttctgtcatggccattttacaattcactgct-tgtttgcatatgttgttaccagacaatataatctcccgcttttttatggcta--tagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA-
||| || | | || | ||| || ||||| | |||| || | ||| || | | | | | | || | || |||||||||||||| | ||| ||||||| ||||||||||||||||| || || || | ||| || ||||| || ||||||||||||||||| ||||| ||||
ttagtgcaaatcgaaggggagatcagtgtactttttcctgctatttttggttacact-ttaattctttatctttgcactcatgatataattggtaactagcTTCCAGATGGTCAACTCAGGGAGAAAATTGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAAG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 7
----gtgtgtatttctgtcatggccattttacaattcactgcttgttt-gcatatgttgttaccagacaa-tataatctcccgcttttttatggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA
||| || | | || || || |||||| ||| | || | | | | | | ||| | | | | |||||||||||||| | ||| ||||||| || |||||||||||||| || || || | ||| || ||||| || ||||||||||||||||| ||||| ||||
attagtgcaaatcgaaggggagatcagagtaatttttcctgctttttttggctacactttaattctttatctttgcgctcatgatatacttgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAA
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 7
gtgtgtatttctgtcatggccattttacaattcactgcttgtttgcatatgttgtt--accagacaatataatctcccgcttttttatggcta----tagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA
||| |||||| | | |||| | || | | || | | ||||| ||| | | | | || | | | || | |||||||| ||||| || ||| |||| | ||||||||||||||||| || || |||||||| || |||||| |||| ||||| |||||||||||||||||||
gtgagtattttcattctt-tcattctgtaaagaagaaatgcattcagtttcttgtttagtgtaacagttttcttttccatgtctctgctgcaacaagtagCTTCCTGATGGTGAGCTCAGGGAAAGAATTGAGAAACTTGCTTCGTCCCTTAAGTTTCCCTTAAAGAAGTTGTTCGTTGTTGATGGATCTACAAGGTCAA
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ36622 (Selaginella moellendorffii), 3'ss of exon 7
gtgtgtatttctgtcatggccattttacaattcactgcttgtttgcatatgttgttaccagacaatataatctcccgcttttttatggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA
|| || | | || | | | | | | | | | | |||| || || ||| | || || | |||||| | || ||| | ||||| || ||||||||||||||||||||||| || ||||| ||||| | |
----------------------------------------gtaagctcacgcacatagtgtaatctcttgaaactgacatcgtaactgttgcagCTCCCGGAAGGATCTTTGCGAAAGCAAATTGAGGATCTGGCTGCCTCTCTGAAATTTCCTTTGAAGAAGCTGTTTGTGGTAGATGGCTCTACCCGAAGCAMapped 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|164229780|gb|EL976434.1|EL976434EST: ACCGCTCTTCAACAAGTTCACTCCT CTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTA
genomic: ACCGCTCTTCAACAAGTTCACTCCTgtgtgtattt ... atggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTA
EST:
gi|164013437|gb|ES075484.1|ES075484EST: CAAGTTCACTCCT CTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTA
genomic: CAAGTTCACTCCTgtgtgtattt ... atggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttgcatatgttgttaccagacaatataatctcccgcttttttatggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA
tctcccgcttttttat CT-rich tract
acaatataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtatttctgtcatggccattttacaattcactgcttgtttgcatatgttgttaccagacaatataatctcccgcttttttatggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA