Sequence
atgc intronic sequence ATGC exonic sequencegttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
Basic information
species | Physcomitrella patens |
transcript | PP1S169_48V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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--------------------------------------------------gtgtgcc-tctgctttgatgcagtatcaaa-atttgcatat-agttt---cattttatagttt----gattttatctactttgttt--gtttga-----tattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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--------------------------------------------ttggcagtctgtaatttcttt--------aatctcac-tttgcaccagcatcttccaaagtacatgatattgatattttt----tttgaccctttcatata-tatatatttcagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 9
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacg-aggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggt-cttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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----------------------------------------------------------cttatttttgtgtagcatgcactgatctgagttttctgttatcct-tttgcaaaca-acatgataccaagatttgtttctaatattttcttccaattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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-------------------------------------------------------------------gtaagttgtaaagaattttagtaatgttttatggatgctgtcaa--catttgtcgttgacatgatgctgatgtat-ctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcat-ctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtat-gcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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------------------------------gtaagatatc-----ccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaa---ataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 8
------gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaa-acgggcatctgtg-----taggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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gtaagatttctttctacccttcaagca---cctttataagaatctcatcaagttctgtttgaaatatacaaggactatcatcatccaattctgtgctttataaggattattatcatccacttctgtgc----tttactgatagtgtttataaattctgttcatcatccagTTGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttact-ttagta-tgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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------------------gtaagatttcttttaacttcttgggcacttcc-ctggcccctgttgtctattggcattgagtgttctatttaga---ttcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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---------------------------------------------------------------------------------------gtgatagttttt-ttctgtatagagaggtagcatttct---tcttgttct--catgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA
upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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---------------------------------------------------------------------------------------gtgagagttttt-ttctgtatagagaggtagcatttct---tcttgttct--catgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAMapped 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|162255349|gb|FC432075.1|FC432075EST: AAATAGCAATCATGACATTGATGGCGTATTTATCTTACGTCTTTGCAGAG CTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATG
genomic: AAATAGCAATCATGACATTGATGGCGTATTTATCTTACGTCTTTGCAGAGgttagctcga ... ttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
atcttac putative branch site (score: 3)
tcttttttgc putative PPT
ttttagaaatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
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