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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATTTGCTATGCCACAGAGTGGAACAGGTGTAAGTGTGGAAGCAGTTGACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctctctctcctcctatagcatcatgccccccccccccctttttttttttttcccctctgtctcttcttgatatctcgagtggttgaagtttgtg...

Basic information

species Physcomitrella patens
transcript PP1S46_324V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA14G08940.1 (Glycine max), 5'ss of exon 2
ATGTATTTGCTATGCCACAGAGTGGAACAGGTGTAAGTGTGGAAGCAGTTGACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctctct-ctcctcctatagcatcatgccccccccccccctttttttttttttcccctctgtctcttcttgatatctcgagtggttgaagtttgtg
|||| ||||| ||||| |||||||| || ||||| || || ||||| ||||| | ||| ||||| || || |||||||||||| | |||||||||||  |||     | | |  |  |  | | |     |        |     |||||||||||         |  | || ||| ||  |    ||       ||| | 
ATGTGTTTGCGATGCCTCAGAGTGGGACCGGTGTCAGCGTTGAAGCTGTTGATCATGTTTTTCAGACTAATATGCTTGATATGTTGAAGCAAACTGGAAGgtgtttttttgtgtttgttttgttgttagttaaagttttcttttttttttttttttagtgaaggagggtttttttgttacttgatttgtacactttttat-

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G36230.1 (Glycine max), 5'ss of exon 2
-ATGTATTTGCTATGCCACAGAGTGGAACAGGTGTAAGTGTGGAAGCAGTTGACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctctct-ctcctcctatagcatcatgcccccccccccccttt--ttttttttttcccctctgtctcttcttgatatctcgagtggttgaagtt-tgtg-------------------------------
 |||| ||||| ||||| |||||||| || ||||| || || ||||| ||||| | ||| ||||| || || |||||||||||| | ||||| |||||  ||||    | |    |  |  | | |  |  |              |||  ||    ||||   ||  ||   || |  || | | |  || ||   ||| | ||                               
GATGTGTTTGCGATGCCTCAGAGTGGGACCGGTGTTAGCGTTGAAGCTGTTGATCATGTTTTTCAGACTAATATGCTTGATATGTTGAAGCAGACTGGAAggtacttttttgggtttgttttgttgttttttttagtgaaggagggtttggttgccgttttttgctgcgtggtttatacatgtgtgggttgttttttgttgtatgatagttgaaacgttggcgttttgtcgttgca
















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|67573473|gb|BJ946297.1|BJ946297
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|67692976|gb|BJ953209.1|BJ953209
EST:     GACCCTGTCTTTCAAACGAAGATGCCTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208388020|gb|DC933140.1|DC933140
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208384664|gb|DC915239.1|DC915239
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|162173753|gb|FC349929.1|FC349929
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208390625|gb|DC937557.1|DC937557
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208378926|gb|DC922772.1|DC922772
EST:     AGATGC-TGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: AGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208400245|gb|DC908906.1|DC908906
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208378125|gb|DC902598.1|DC902598
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|22131888|gb|BQ826859.1|BQ826859
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208395571|gb|DC928986.1|DC928986
EST:     GACCCTGTC-TTCAAACGAAGATGCCTGATATGCTCCAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208368927|gb|DC947485.1|DC947485
EST:     AAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: AAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|67570106|gb|BJ942930.1|BJ942930
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|18329512|gb|BJ161518.1|BJ161518
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208362822|gb|DC950622.1|DC950622
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|162150910|gb|FC327390.1|FC327390
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|67696853|gb|BJ957086.1|BJ957086
EST:     AGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: AGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|67569711|gb|BJ942535.1|BJ942535
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208387484|gb|DC933347.1|DC933347
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|18327697|gb|BJ159700.1|BJ159700
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGT
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGT
EST: gi|208369314|gb|DC955859.1|DC955859
EST:     CGAAGATGCCTGATATGCTCAAGCAAACTNGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: CGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|100420708|gb|BY993475.1|BY993475
EST:     GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|162150909|gb|FC327389.1|FC327389
EST:     TCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: TCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|18335934|gb|BJ167955.1|BJ167955
EST:     TCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: TCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
EST: gi|208364180|gb|DC947284.1|DC947284
EST:     GACCCTGTC-TTCAAACGNAGATGCTTGATATGCTCAAGCAAACTGGTCG                         ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG
genomic: GACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 25 (upstream exon), 35 (downstream exon)
Score: 7

ATGTATTTGCTATGCCACAGAGTGGAACAGGTGTAAGTGTGGAAGCAGTTGACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctct ... tgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTATTTGCTATGCCACAGAGTGGAACAGGTGTAAGTGTGGAAGCAGTTGACCCTGTCTTTCAAACGAAGATGCTTGATATGCTCAAGCAAACTGGTCGgtagggctctctctcctcctatagcatcatgccccccccccccctttttttttttttcccctctgtctcttcttgatatctcgagtggttgaagtttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA