Sequence
atgc intronic sequence ATGC exonic sequencegtacacattctttcaaagtattctatgatctatttctatccagaatgctggtagttcgacagtttttgtcttgagcattgccatggaaagcattctaggttagaattgtatttttataagttgtgatagtgctactggcttaagcttcgaggaatggggaatagcttgaagcctaacaaatttttttgtgagatcagATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTCGAGATTGTCCAGGATGCAAATGTTCCGGGCATCG
Basic information
species | Physcomitrella patens |
transcript | PP1S22_429V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 10
gtacacattctttcaaagtattctatgatctatttctatccagaatgctggtagttcgacagtttttgtcttgagcattgccatggaaagcattctaggttagaattgtatttttataagttgtgata-gtgctactggcttaagcttcgaggaatggggaatagcttgaagcctaacaaatttttttgtgagatcagATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTCGAGATTGTCCAGGATGCAAATGTTCCGGGCATCG
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------------------------------------------------------------------------------------------tgatcaattattagtcattagctttggaaaatacagtatatgcaaagaatttccacctt------ttagaagaaacatgatgacttacccattgtgtcttttg--cagATGCTGTCTTCAAAGGATTTGAATTTTGTGGGCTACACGTACAAGAACTTCGAACTTGTGAATGATCCTGAAGTACTTGGAATGG
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ16108 (Selaginella moellendorffii), 3'ss of exon 10
gtacacattctttcaaagtattctatgatctatttctatccagaatgctggtagttcgacagtttttgtcttgagcattgccatggaaagcattctaggttagaattgtatttttataagttgtgatagtgctactggcttaagcttcgaggaatggggaatagct-tgaagcctaacaaatttttttgtgagatcagATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTCGAGATTGTCCAGGATGCAAATGTTCCGGGCATCG
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----------------------------------------------------------------------------------------------------------------------------------gtaagtacttc--gcgttgaatcattcggcaaagctacaaagtgttatttacttcctcgattctttagATGCTTCCTTCCAAGGACGTCAACTTTGTTGGCTACACGTACAAGAACTTCGAGATCATCCAAGACTCGCAATTGCCCGGTGTTGMapped 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|37849883|gb|BJ607891.1|BJ607891EST: AGCGATTCCCAGATACCATCATCCACAAGATCAGGACCATGGAGAAAG ATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTC
genomic: AGCGATTCCCAGATACCATCATCCACAAGATCAGGACCATGGAGAAAGgtacacattc ... gtgagatcagATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttcgaggaatggggaatagcttgaagcctaacaaatttttttgtgagatcagATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTCGAGATTGTCCAGGATGCAAATGTTCCGGGCATCG
gcctaac putative branch site (score: 2)
tttttttgt putative PPT
taacaaatttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacattctttcaaagtattctatgatctatttctatccagaatgctggtagttcgacagtttttgtcttgagcattgccatggaaagcattctaggttagaattgtatttttataagttgtgatagtgctactggcttaagcttcgaggaatggggaatagcttgaagcctaacaaatttttttgtgagatcagATGCTGTCGTCAAAGGACGTGAACTTTGTAGGGTACACGTACAAGAATTTCGAGATTGTCCAGGATGCAAATGTTCCGGGCATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG