Sequence
atgc intronic sequence ATGC exonic sequencegtgctgatacatgattacattcacaagatttattttatcttttgaattgttgtgaatgaagcttagccatattactattttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78920.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 4
-----------------gtgctgatacatgattacattcacaagatttattttatcttttgaattgttgtgaatgaagcttagccatattactattttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
| ||| || || || | | || || |||| | || || | | | | ||| |||| || ||| | |||| | | ||||| || || ||||| ||| | || ||||| || || || || || ||| ||||||||||||| || |||||||||||||||||||| |||
gtgacttcaaaaattatatatatatatatatatatatatatgctgtgaatcttttcttctacctt-ttacttgttctgatctgtcat-ttac-atcttgtttcagGACAACTTCTGCATACATCACTGTAGCTTCTTTCCTTTTAGGTGCCCTTTGTTCGGGTGTTGCTGGATATGTAGGGATGTGGGTGTCAGTTCGTGCCAAT
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 4
gtgctgatacatgattacattcacaagatttattttatcttttgaat-tgttgtgaatgaagcttagccatattactattttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
| |||| || | | ||| | | | | ||| ||| | | || | | | | ||| |||| || || | ||| | | ||||| || || || || ||| | || ||||| || || || || || ||| ||||||||||||| || |||||||||||||||||||| |||
-----gtgacatcataaattatacatgctgtgaatcttctcttgtaccttttacttgttctgatctgtcat-ttac-atcctgttttagGACAACTTCTGCATACATCACCGTAGCTTCTTTCCTTTTAGGCGCCCTTTGTTCCGGTGTTGCTGGATATGTAGGGATGTGGGTGTCAGTTCGTGCCAAT
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 4
gtgctgatacatgattacattcacaagatttattttatcttttgaattgttgtgaatgaagcttagccatattactattttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
||| | | | || | ||| | | || | | ||| |||||| |||| | | | | ||| | |||| | | |||| ||||||||||||||||| ||||| | |||||||| || ||||| |||||||| |||||||||||||||||||| || ||||| ||
gtgataacagatttacatattagattgcatctcttccacatcaatattcttgtga-tgaacgatcctgttctggtcctgttgatacagGTCAACAACTGCATATATTACTGTTGCTGCCTTTCTCCTAGGGGCTCTTTGTTCAGGAATTGCTGGGTATGTTGGAATGTGGGTGTCGGTACGTGCAAACMapped 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|125186168|gb|EL201122.1|EL201122EST: AGGCTGCTGGTTTAGGAAG GGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATG
genomic: AGGCTGCTGGTTTAGGAAGgtgctgatac ... tttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATG
EST:
gi|164148937|gb|ES127039.1|ES127039EST: TATCTATTCCGTAGCTTAACTCCCCAGCAAGAGGCTGCTGGTTTAGGAAG GGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGC
genomic: TATCTATTCCGTAGCTTAACTCCCCAGCAAGAGGCTGCTGGTTTAGGAAGgtgctgatac ... tttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatcttttgaattgttgtgaatgaagcttagccatattactattttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
ctatttt CT-rich tract
atattactatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgatacatgattacattcacaagatttattttatcttttgaattgttgtgaatgaagcttagccatattactattttgctgcagGGCGATGTCTGCTTATATTACTGTTGCTGCATTTCTTTTGGGGGCTCTATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA