Sequence
atgc intronic sequence ATGC exonic sequencegtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08080.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 3'ss of exon 10
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
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------------------------gtgacttttttgacataagcactt------atttactaatctgat-ttaatccatatgcttgtgagctcg-------agttaatgtgcctaattac----tccattccttgtttttgccttgtagATATTCATGGATATGGCAGTTTTGGTTGATGCTCAAGGAGACATGATCAACAACATAGAGACACAT
upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv08s0032g00440.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
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-----------------------------------------atggaagaaagaagtgtttaaatcaaaggatataagttttatcaaaactcagcttgtgcaaatacatgcagtttta--------taaatacattcctgtctcgtgcagATATTCTTAGATATGGCGGTGTTGGTAGATGCACAGGGGGACATGCTTGACAATATAGAATCACAG
upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ11731 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
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---------------------------------------------------------------------------------gtatac-aagagaaacaaaaaactttcgtgccaagaatctca-ctgtgcgtttcc---ttcgctgcagATATTCTTGGATATGGCTGTCCTCGTTGAGGCGCAGGGAGAGATGCTGGACAACATAGAAACACAA
upper sequence: AT5G08080.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ22520 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
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---------------------------------------------------------------------------------gtttac-aagagaaacaaaaaactttcgtgccaagaatctca-ctgtgcgtttcc---tttgctgcagATATTCTTGGATATGGCTGTCCTCGTTGAGGCGCAGGGAGAGATGCTGGACAACATAGAAACACAAMapped 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|125314891|gb|EL328976.1|EL328976EST: GCTGTCAGAGACTTGGAAAAGAAACTTCTTGACTTACAACAA AATATTCTTGGATATGGCAGTTTTGGTTGATG
genomic: GCTGTCAGAGACTTGGAAAAGAAACTTCTTGACTTACAACAAgtatgttgga ... tttcttgcagA-TATTCTTGGATATGGCAGTTTTGGTTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
gcctaaa putative branch site (score: 3)
ttccccttttcttgc putative PPT
aattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttggatttcatatttccttatgaacatctttgaaccagagtttgatgcaatctgttaatcaaacatttttttcttcgtctgttaagtcgttgtatgaattcattcgcctaaagacagatctaagaggttccccttttcttgcagATATTCTTGGATATGGCAGTTTTGGTTGATGCACAAGGAGAAATGCTTGACAATATAGAATCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA