Sequence
atgc intronic sequence ATGC exonic sequenceGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcacttacacttatctcctttgcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttg...
Basic information
species | Physcomitrella patens |
transcript | PP1S3_299V6.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S3_299V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 5'ss of exon 5
GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcacttacacttatctcctttgcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttg-------------------------------------------------------------
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GAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAGgtgat-tttctcttatggtacctttattgggaacatgttatcttattgaattcc--actttcgtaggatgttcatctactttgagacatgtaaaaatgtgttaatgtttcacaataagcattctgaccctctgatgcgaacaagttcatgctatgaatcag
upper sequence: PP1S3_299V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcactta--cacttatctccttt-gcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttg-------------------------------
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GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactcta-----gtcacggcgtttcatattttgt-atgtgaaaatgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
upper sequence: PP1S3_299V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ36938 (Selaginella moellendorffii), 5'ss of exon 5
GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcacttacacttatctcctttgcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttg
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GAGTTAATGCTGATGATGTTCGTGTGACTGTTGCTGCTCCAGCCGCGAGAGGAGAGGCAAACAACGAACTTCTGGAGTACATGGCAAAGgtaa-atcaaaccaaaaaacattcgctcgctattaagccaacttgtaacag-------------------------------------------------Mapped 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|37852757|gb|BJ610765.1|BJ610765EST: CAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG GTGCTGGGACTAAGATTGACACAAATGACTCTCCAGCGAGGTTGGAACAAT
genomic: CAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttc ... taagttacagGTGCTGGGACTAAGATTGACACAAATGACTCTCCAGCGAGGTTGGAACAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcacttacacttatctcctttgcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT