Sequence
atgc intronic sequence ATGC exonic sequence...ttaaaaatctccttagcgagtttacatggattggttgatatttccatttgcattttcagccaattagtctctcgttactgattattttagtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40760.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
ttaaaaatctccttagcgagtttacatggattggttgata--tttccatttgcattttca-gccaattagtctctcgttactgattatttta-gtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC
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---aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatgataacacttta-tggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
ttaaaaatctccttagcgagtttacatggattggttgatatttccatttgcattttcagccaattagtctctcgttac---tgattatttta--gtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC
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---actctcttttagataaggtcctctatattttgtgaggtttctgtattg--tcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCCMapped 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|164089728|gb|ES206500.1|ES206500EST: GAGAAAGTGAAG GTGC-TCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAA
genomic: GAGAAAGTGAAGgtgaacaaat ... tgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgcattttcagccaattagtctctcgttactgattattttagtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC
tactgat putative branch site (score: 2)
ttactgattatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaaaatctccttagcgagtttacatggattggttgatatttccatttgcattttcagccaattagtctctcgttactgattattttagtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC
ttaaaaa
- - - - - - - - - - - - - -ggattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cagccaa