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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCACACCCATTGTTACGTCAGGGCTCGTTATGCAACTTTTGGCTGGATCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgattatgtcttccatttgaactctttgaaatacttcttgctatttgtacatccctgttggtgttcccattgagcttattttgagaccacaccag...

Basic information

species Physcomitrella patens
transcript PP1S114_48V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 1
GTATCACACCCATTGTTACGTCAGGGCTCGTTATGCAACTTTTGGCTGGATCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgattatgtctt-----ccatttgaactc---tttgaaatacttcttgctatttgta--catccctgttg--gtgttcccattgagcttattt-tgagaccacaccag---------------------------------------------------------
|||| || || ||||| || || ||| | || ||||||||| | | |||||||||| ||||||| |||||||||||||| || |||||  | || ||  |||||||| |    | ||       || | | ||    |||   | | ||||  || || ||     |  |   ||  || || |  | |   || | | | | |      ||                                                          
GTATTACTCCAATTGTGACATCTGGGATGGTAATGCAACTTCTTGTTGGATCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtgttgtcttattaaaaataatgtaaccttcaatttatcacaattctaactgttggtggttgtttcatctgcagtctttctgtagcatttctctatcatagtctgtcaaagtagattataaaccttctgatttgtattgtgatgcacattgcacttctttactcag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G130987_T04 (Zea mays), 5'ss of exon 1
GTATCACACCCATTGTTACGTCAGGGCTCGTTATGCAACTTTTGGCTGGATCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgattatgtcttccat----ttgaactctttgaaatacttcttgctatttgta---catccctgttggtgttcccattg-agcttat-----tttgagaccacaccag-----------------------------------------
|||| || || ||||| || || ||  | || ||||||||| | |  ||||||||| ||||||| |||||||||||||| || |||||  | || ||  |||||||| || | | |   |     |||   ||||  |    |    | ||| | |||     || || |      | |||| | || ||||     ||     |   |                                             
GTATTACTCCAATTGTGACCTCTGGTATGGTAATGCAACTTCTTGTCGGATCGAAGATCATTGAAGTTGACAACAGTGTGAGAGAGGATCGTGCTCTGCTgtaagtg-ttgtctttctaaaaatattgtgatcttcaattatcacaattctaatcgtagcatttctctatcaagtctgccatagtagattataaaccttctgatctgtatttaatatatttgtattgtgatgcacattgcatttctttactcag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA06G32680.1 (Glycine max), 5'ss of exon 2
GTATCACACCCATTGTTACGTCAGGGCTCGTTATGCAACTTTTGGCTGGATCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgattatgtcttccatttgaactctttgaaatacttcttgctatttgtacatccctgttggtgttcccattgagcttattttgagaccacaccag
| ||||| |||||||| || || ||||| || |||||||||||||||||||||||| ||||||| || ||||||| ||| ||||||||  | || |||||||||||   | | | |     |   | |  ||    |  | | ||   |||  || |  |  || |   | ||  |||  |||  | |   |       |
GAATCACCCCCATTGTGACTTCTGGGCTGGTAATGCAACTTTTGGCTGGATCGAAGATCATTGAAGTGGACAACAATGTAAGGGAGGATCGTGCTCTCTTgtaagtatctttatttctgtatcttattaattttcttggtacatgtgttttacacttttccttttgcaattcctgtgattttagctggttgcttttgtgg

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 2
GTATCACACCCATTGTTACGTCAGGGCTCGTTATGCAACTTTTGGCTGGATCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgattatgtcttccatttgaactctttgaaatacttcttgctatttgtacatccctgttggtgttcccattgagctta-ttttgagaccacaccag
| ||||| || ||||| || || ||||| || |||||||||||||||||||||||| ||||||| || ||||||| |||  |||||||  | || |||||||||||   | | | |     |   | |  ||    |  | | || | |||  |  |  |  || |   | ||  |||  |||  | |  |         |
GAATCACCCCTATTGTGACATCTGGGCTGGTAATGCAACTTTTGGCTGGATCGAAGATCATTGAAGTGGACAACAATGTACGGGAGGATCGTGCACTCTTgtaagtatctctatttctgtatcttatttattttcttggtacatgtt-tttacatttttccttttgcaattcctgtgattttagctgtttgcttgtggttg

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|100362213|gb|BY947246.1|BY947246
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|18324734|gb|BJ156729.1|BJ156729
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|100379552|gb|BY949826.1|BY949826
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|208377058|gb|DC936804.1|DC936804
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|100364799|gb|BY947914.1|BY947914
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTG                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|100372241|gb|BY985502.1|BY985502
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCNTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|100397995|gb|BY954036.1|BY954036
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|162185703|gb|FC361557.1|FC361557
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|162179032|gb|FC356433.1|FC356433
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|100404142|gb|BY955276.1|BY955276
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|162172637|gb|FC348018.1|FC348018
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|162166591|gb|FC343483.1|FC343483
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
EST: gi|100369767|gb|BY967377.1|BY967377
EST:     TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTT                         GAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT
genomic: TCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgatt ... tgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCACACCCATTGTTACGTCAGGGCTCGTTATGCAACTTTTGGCTGGATCGAAGCTCATTGAGGTTGACAACAGTGTTAGGGAGGACAGAGCCCTCTTgtaagtgattatgtcttccatttgaactctttgaaatacttcttgctatttgtacatccctgttggtgttcccattgagcttattttgagaccacaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA