Sequence
atgc intronic sequence ATGC exonic sequenceATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
Basic information
species | Physcomitrella patens |
transcript | PP1S165_119V6.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTCCGCAAGGAGCCATTCTTCTATGGTCATGATAACCATGATCAACTTGTCAAGATCGCAAAGgta-agtcccagtt------tgattctggcctctcacatttctcaagggaaaaaaaatggtttggtatg------cctgataaaatgtttagttatgc-aactcgtgttttgga----------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacat-----agatttgccttcaagcagttatatat--cactttttatttattttgt-ataaaaagt-catattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctcagcttgtttatgttaaaagatgatgttcatacaagaatgaaatgcatttcatgtttagcttatcattcatactgtacactatggtttatc---------------------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaa-agtcatattactgtctttcgcaacgc-caagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgt-----------------aaggattcgttt------gattgt---tcattccacatgtttctgggataaagtagatgttttgctatggaccttagtatgcaacttgtggtttgaa---tatttttaga---------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgcc---ttcaagcagtta--tatatcactttttatttattttgtataaaaa--gtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgta-agcgttagtttgattgttcattccacatgtttctgcggtaaagtagatgttttggtatggaccttagatgcaactcgtggtttgactatttctagaa------------------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 5
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattcagtctatttgttc-tttgcaatgaactagtcaactagc-tatgttgtttacatttcccatgtcatgtagccagagatttcatttctgtcaag----------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgt----tatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgca-----agtgctgattattgttacatcctttatcag-------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgta-agggaagcctgggaggtggacttgagtttgtgc-----catattgttatgtgtgt---ttgggtgataactcat--tgctgctttgctctggtcctggtgttgtttt-------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgta-agggaagcctgggaggtggacttgagtttgtgcca--gattgttaagttatgtatgttt-gagtgataactcat--tgctgctttgctctggccctggtgtt------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcag-----ttcat-acatagatttgccttcaagcag-ttatatatcactttttatttattttgtataaaaagtcatattac-tgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAGgtaacattacaaaagctttcatcatgtctcgtctcctctgaacagattttacatt-cctccaagttata--gctaaaaatacgattctatgtatttataactatggcag-----------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATCTTTCGCAAGGAACCATTCTTTTATGGTCATGACAATCATGATCAGCTTGTCAAGATTGCCAAGgtatgtttg----------gctaaatgatcttaaaa----tttaaggcatagtcttttcatatcat-tcaaaggttctgccact-----ttgccaaaacagcatgtatttcaagtactag----------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatca-ctttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAGgt--aatgacaat-cgtgtgtttagctaaattatgttatctcctggtggtcctgttttttctttaatccagtaagcaatgccatggttgagtgta---ctcaattg-------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATTTTCCGCAAGGAGCCATTTTTCTACGGGCATGATAATTATGATCAACTGGTTAAAATAGCTAAGgta-agtgttaaatttctc-----tctgtcaactagtagatatcaggaacatctgaattcc--------aacagcttaatta-tatcattttgaaagtgagtctttgcagagagc---------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgt----------tttaaacgcagaat-gtctgtttcttgctgtttttgacgttg-gcttgtggtgtttag------------------------------------------------------------------------
upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
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ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgt----------tttaaacccagaat-gtctgtttgttgctgtttttgacgttg-gcttgtggtgtttag------------------------------------------------------------------------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|37831146|gb|BJ589158.1|BJ589158EST: CATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG GTGTTGGGAACTGATGAATTGAATTCCTATCTAAACAAATACCGCCTAGAG
genomic: CATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggc ... ctgataccagGTGTTGGGAACTGATGAATTGAATTCCTATCTAAACAAATACCGCCTAGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA