Sequence
atgc intronic sequence ATGC exonic sequenceCAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66880.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 5'ss of exon 5
CAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgta-----------tcacaaatgattttgttcttttg-----gtatcagaaact--atacacttgtggttcct----ccattgt-catgttcaaatgtgtttttaaagt------gtttgcttatgcatttctttttgacag-----------------
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CAAATTTGCCATCGTGATTTGAAATTGGAAAACACTTTGTTGGATGGAAGTCCTGCGCCTAGGCTGAAAATCTGTGATTTTGGGTATTCAAAGgtgagatttactcgtttcttgtcgtttcattgcgttgaagcagctcgaggaagtggataggtttaccattgctgaggctataacacatgtttcactggtccttttaaatcttacagtttttttattaattgttttttgacgggtttctgttgattgcag
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 5'ss of exon 5
CAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgt-atcacaaatgatt---ttgttcttttggtatcag----aaactatacacttgtggttcctccat-tgtcatgttcaaatgtgtttttaaagt---gtttgctt-atgcatttctttt-tgacag-------------------------------------------------------
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CAAATCTGCCACCGAGATCTGAAGTTAGAGAACACGTTGCTTGATGGAAGCCCAGCTCCTAGGCTGAAAATATGTGATTTTGGATATTCGAAGgtgagttttaatgattcctttggtagttgggaatgatttctagactttacacttaaaactggacgatgtctcatggacga-tgtctcagttgggttgagatagctcgatggattggtattattacacgctcgaatcaatgatgtgttgttctacaatttttgactcttcgtttcgattgcag
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 5'ss of exon 5
CAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgta--tcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccatt-----gtca-tgttcaaatgtgtttttaaagtgttt--gcttatgca-----tttctttttgacag-----------------
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CAAATTTGTCACCGTGATTTGAAATTGGAGAACACATTGCTGGATGGAAGTCCTGCACCTAGACTGAAAATCTGTGATTTTGGATATTCAAAGgtaagcttctcgtctgtttgtttgtttgttttttg--attgttccgctgagatagctcaatgaagtagtcaactttcacaactgatgagagcacatcacaggttgtacgaattttctatctttgatggttttctgtttattgcagMapped 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|124929739|gb|EL007258.1|EL007258EST: ATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAG TCTTCTGTTCTTCATTCACAACCAAAG
genomic: ATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgtatcacaaa ... tttttgacagTCTTCTGTTCTTCATTCACAACCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAAATTTGCCATCGTGACCTGAAGCTAGAGAATACATTGTTGGATGGAAGTCCTGCTCCTCGATTAAAAATTTGTGATTTTGGATATTCAAAGgtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacag
- - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC