Sequence
atgc intronic sequence ATGC exonic sequencegtatgtagagaatctgtttcatggagcctatggactggttgtattcttgtttttttctaacttgttgttaatactctactttttttcatgtgctgtgaagCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 4
gta--tgtagagaatc-tgtttcatggag----cctatggac-tggttgtattcttgtttttttc--taacttgttgttaatactctactttttttcatgtgctgtga-agCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG
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gtaattgttctgaaccctgacgcgcgtggttttcctatcagcattgaagttttctggatttgtacagtgcttccttatgacctgactacaatttttctggtaacattttagCAAATTTGTCACCGTGATTTGAAATTGGAGAACACATTGCTGGATGGAAGTCCTGCACCTAGACTGAAAATCTGTGATTTTGGATATTCAAAG
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------gtatgtagagaatctgtttcatggagcctatggactggttgtattcttgtttttttctaacttgttgttaatactctactttttttcatgtgctgtgaagCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG
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gtgatttcctgaccctttaagtatcgcaatcttattttatgatttgagttatcgggtattttctttcggtttgttcttttcctcactctgattatgcatctgcatgtgaattttccagCAAATCTGCCACCGAGATCTGAAGTTAGAGAACACGTTGCTTGATGGAAGCCCAGCTCCTAGGCTGAAAATATGTGATTTTGGATATTCGAAG
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtagagaatctgtttcatggagcctatggactggttgtattcttgtttt----tttctaacttgttgttaatactc-----tactttttttc--atgtgctg-------tgaagCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG
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----gtaatgtttctgaaccttgaatcttgtgtgttgtttcaattttgagattggattttttgagttgtgattagttttccctcctgcctgatcccgaatgtgccggttcaattgcagCAAATTTGCCATCGTGATTTGAAATTGGAAAACACTTTGTTGGATGGAAGTCCTGCGCCTAGGCTGAAAATCTGTGATTTTGGGTATTCAAAGMapped 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|124890407|gb|EH969309.1|EH969309EST: GGTTCTTCTTTCAGCAGCTTCTATCTGGAGTCAGTTATTGTCATTCGATG CAAATTTGCCATCG
genomic: GGTTCTTCTTTCAGCAGCTTCTATCTGGAGTCAGTTATTGTCATTCGATGgtatgtagag ... tgctgtgaagCAAATTTGCCATCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtttttttctaacttgttgttaatactctactttttttcatgtgctgtgaagCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG
ttttttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtagagaatctgtttcatggagcctatggactggttgtattcttgtttttttctaacttgttgttaatactctactttttttcatgtgctgtgaagCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC