Sequence
atgc intronic sequence ATGC exonic sequencegtgatcatacatcttctacagaatcttttcttttatcttttgtgttgttataaataaaactcaaatgtataactttgtgcttcagGACAATGTCTGCATACATTACTGTTGCTGCATTTCTTTTGGGTGCGCTATGTTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 4
---------------------------gtgatcatacatcttctacagaatcttttcttttatcttttgtgttgttataaataaaactcaaatgtataactttgtgcttcagGACAATGTCTGCATACATTACTGTTGCTGCATTTCTTTTGGGTGCGCTATGTTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
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gtgacttcaaaaattatatatatatatatatatatatatatgctgt-gaatcttttcttctaccttttac-ttgttctgat-----ctgtcatttacatctt---gtttcagGACAACTTCTGCATACATCACTGTAGCTTCTTTCCTTTTAGGTGCCCTTTGTTCGGGTGTTGCTGGATATGTAGGGATGTGGGTGTCAGTTCGTGCCAAT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 4
--gtgatcatacatcttctaca----gaatcttttcttttatcttttgtgttgttataaataaaactcaaatgtataactttgtgcttcagGACAATGTCTGCATACATTACTGTTGCTGCATTTCTTTTGGGTGCGCTATGTTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
| |||||| || | | ||||||| |||| || ||||| ||||| | | || || || | | | | || ||||||| ||||||||||| || || ||| | || ||||| || || || ||||| ||| ||||||||||||| || |||||||||||||||||||| |||
gtgacatcataaattatacatgctgtgaatcttctcttgtaccttttac-ttgttctgat-----ctgtcatttacatcct---gttttagGACAACTTCTGCATACATCACCGTAGCTTCTTTCCTTTTAGGCGCCCTTTGTTCCGGTGTTGCTGGATATGTAGGGATGTGGGTGTCAGTTCGTGCCAAT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 4
gtgatcatacatcttc-tacagaatcttttcttttat-cttttgtgttgttataaataaaactcaaatgtataactttgtgcttcagGACAATGTCTGCATACATTACTGTTGCTGCATTTCTTTTGGGTGCGCTATGTTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
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gtgataacagatttacatattagattgcatctcttccacatcaatattcttgtgatgaacgatcctgttctggtcctgttgatacagGTCAACAACTGCATATATTACTGTTGCTGCCTTTCTCCTAGGGGCTCTTTGTTCAGGAATTGCTGGGTATGTTGGAATGTGGGTGTCGGTACGTGCAAACMapped 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|125217116|gb|EL231199.1|EL231199EST: ACTTGTTCCGTTAACTTAACCCCCCAGCAAGAGGCTTCTGGTTTAGGAAG GACAATGTCTGCATACATTA
genomic: ACTTGTTCCG-TAACTTAACCCCCCAGCAAGAGGCTTCTGGTTTAGGAAGgtgatcatac ... tgtgcttcagGACAATGTCTGCATACATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcttttgtgttgttataaataaaactcaaatgtataactttgtgcttcagGACAATGTCTGCATACATTACTGTTGCTGCATTTCTTTTGGGTGCGCTATGTTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
gtataac putative branch site (score: 3)
ttataaataaaactca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatcatacatcttctacagaatcttttcttttatcttttgtgttgttataaataaaactcaaatgtataactttgtgcttcagGACAATGTCTGCATACATTACTGTTGCTGCATTTCTTTTGGGTGCGCTATGTTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA