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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga...

Basic information

species Physcomitrella patens
transcript PP1S364_56V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 5'ss of exon 5
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtccta-ttagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga
|||||||| ||||| || ||||||  ||| ||||||||||||||||||||||| ||||| ||| |  | || |||||||||||||||||||| |||||||||||||| |  ||     ||  |   |   |||| |    ||| ||  |  || ||     | | ||  |  |   ||  |                    
AAAGGTCTGGATGTTGATACTCTTTATGTGTCCCACATTCAAGTTAACCAGGCCCAGAAGCAGAGGCGCCGTACCTACCGTGCTCATGGACGCATCAACCgtaagtt-tgtcaatacctttttgtatgctctttgtagagttcggtgatgctttgtctcatgagcaaatgatactttgcag--------------------

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G126594_T02 (Zea mays), 5'ss of exon 5
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagt-tatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga
||||| |||||||| || || ||   ||| || |||||||||||||| ||||| ||||| |||||  |  | || ||||||||||||||||| ||||||||||||| ||||  |      |    | || ||| |  |||   |||| ||  |  |   ||||  ||        ||   |    | |||||  | ||   
AAAGGACTTGATGTGGATACCCTCTATGTGTCGCACATTCAAGTTAATCAGGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttct--tcatttggagcttaac-------attctgtttgcctacctggtccag--

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga--
|||||||||||||| || || ||   ||| || ||||||||||| |||||||| ||||| |||||  |  | |||||||| |||||||| || ||||||||||||| |  |    |||  | || | ||    ||||| |   | | ||||| |     |||  |||               ||| ||||||  |  ||   
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgcta-tgctatgaacaggt-tactatttgc----agcttaag---------------atcctacctacctggtgcag

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G119169_T01 (Zea mays), 5'ss of exon 6
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga
|||||||||||||| || || ||   ||| || ||||||||||| |||||||| ||||| |||||  |  | |||||||| |||||||| || ||||||||||||| |  |    |||  | || | ||    ||||| |                                                            
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgcta-tgctatgaacag----------------------------------------------------------

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 5'ss of exon 4
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga
|||||||| ||||| ||  | ||     |||| ||||| ||||| |||||||||||||||||  |  | || || ||||| ||||||||| | |||||||||||||| |     | ||  | |     |  | | | ||  |   |    | | || | |  ||||                 |  ||  | |||     
AAAGGTCTGGATGTTGATTCACTCTACATATCTCACATCCAAGTGAACCAGGCACAGAAACAAAGGCGCCGCACATACCGGGCTCATGGAAGAATCAACCgtaagtt-tgtttcctttcaaatctagcatttgtgtaatggttgttttcctaaatgttaacaggaacc---------------ttctatttgtttggcag

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|162192863|gb|FC370182.1|FC370182
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|7046864|gb|AW476808.1|AW476808
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|162271131|gb|FC447146.1|FC447146
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTTTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|67721496|gb|BJ971755.1|BJ971755
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|18350729|gb|BJ182780.1|BJ182780
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|37849723|gb|BJ607731.1|BJ607731
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|162239738|gb|FC417137.1|FC417137
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|37830055|gb|BJ588067.1|BJ588067
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|18331333|gb|BJ163343.1|BJ163343
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGA
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGA
EST: gi|18364318|gb|BJ196391.1|BJ196391
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAA
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAA
EST: gi|162275627|gb|FC451642.1|FC451642
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|162265094|gb|FC440973.1|FC440973
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|37832810|gb|BJ590822.1|BJ590822
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|37851335|gb|BJ609343.1|BJ609343
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|37836617|gb|BJ594625.1|BJ594625
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|13250457|gb|BG361360.1|BG361360
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACACTGAGCTCGTCCTCTCATAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|162239739|gb|FC417138.1|FC417138
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
EST: gi|37841405|gb|BJ599413.1|BJ599413
EST:     GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG
genomic: GGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatc ... cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGTCTTGATGTAGACACTCTTGTTGTATCCCACATTCAAGTTAACCAGGCACAGAAACAGCGTAGACGAACCTACCGTGCTCATGGACGTATCAACCgtaagttatcccatcgttttacttggttagctttatgatcttctgtcctattagtgctgagcggaagggcgatgatgacgaaatcttacctatttcatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA