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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgacgctgcagaggatgcagaatgtaagtgggttgcatcgtactattctctagatattaatgatattaacctacattaatggttgtaatgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA

Basic information

species Physcomitrella patens
transcript PP1S46_324V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G033626_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------ttcgacgctgcagaggatgcagaatgt--aagtgggttgcatcgtacta-ttctctagatattaatgatattaacctacattaatggttgtaatgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA
                                                                              |   | | |||    | |     | |  ||     ||| ||| ||  |  |   |   |     |  ||  ||   |  | |     | |  | |||  |||||| | |||||||| || ||  |||||||||||||||| | ||| ||||| ||||| ||||| || || ||||||||||| |||||| | ||||| ||||
gtaagtactaagtaatattgtatcatatcttggcctgcatgacaggttttttctatcgcacaatgcatgggggctgtcttacccccgcaagtcaagtttttttttaaaaaatattgtatcatatgaacttgttttgttcctttattaaaaaatgatttgaccatatctgttctttatcagGCTCTTATCCATGGGTTGAATAGACACTACTATTCAATTGCAATCAATTACCGGAAAAATGAGCTTGAGGAGAAAATGCTGTTGAACTTGCACAAAAAGA

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G446426_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------ttcgacgctgcagaggatgcagaatgtaagtgggttgcatcgtacta-ttctctagatattaatgatattaacctacattaatggt-tgtaatgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA
                                                                               |   | | |||    | |     |  || |   ||| ||| ||  |  |   |   |     |  ||  ||   |  || |   | | |  | |||  |||||| | ||||||||  | ||  |||||||||| ||||| | ||| ||||| ||||| ||||| || || ||||||||||| |||||| | ||||| ||||
gtaagtactaagtaatattgtatcatatcttggcatgcatgacaggtttttttctatcgcacaatgcatgggggctgtcttacccccgcaagtcaagtttttttaaaata--ttgtatcatatgaacttgttttgtccctttattaaaaaatgattttgaccatatctgttctttatcagGCTCTTATCCATGGGCTGAATAGACACTACTACTCAATTGCAATCAATTACCGGAAAAATGAGCTTGAGGAGAAAATGCTGTTGAACTTGCACAAAAAGA

upper sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ33925 (Selaginella moellendorffii), 3'ss of exon 4
ttcgacgctgcagaggatgcagaatgtaagtgggttgcatcgtactattctctagatatt-aatgatattaac-ctacattaatggttgtaatgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA
                                                        ||   ||  | |  | | ||||||  ||| ||      ||||||||||| | |||||||| |||||||| |||||||| || ||||  || || ||||| ||||  || || || |||||||||||  | ||||| ||||||||||
-------------------------------------------------------gtaccgaaaaacaaaagctctacatagatgattc---gttttcacagGCTCTGATCCATGGTTTAAACCGGCACTACTACTCGATCGCGATCAACTATCGCAAGACCGAGCTGGAGGAGAAAATGCTGCTCAACCTGCACAAGAAGA

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:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGAT
EST: gi|67692976|gb|BJ953209.1|BJ953209
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|162224586|gb|FC400482.1|FC400482
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|18337375|gb|BJ169399.1|BJ169399
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208390625|gb|DC937557.1|DC937557
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTT-AATCCATG
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATG
EST: gi|208378926|gb|DC922772.1|DC922772
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208400245|gb|DC908906.1|DC908906
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTANTCCATGGATTAAACCGACACTACTATTCA-TCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|162224587|gb|FC400483.1|FC400483
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208378125|gb|DC902598.1|DC902598
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATT
EST: gi|208395571|gb|DC928986.1|DC928986
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208368927|gb|DC947485.1|DC947485
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208362822|gb|DC950622.1|DC950622
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATCCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|162150910|gb|FC327390.1|FC327390
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|37843465|gb|BJ601473.1|BJ601473
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|67696853|gb|BJ957086.1|BJ957086
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208387484|gb|DC933347.1|DC933347
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGAT-AAACCGACACTACTATTCA-TCGGA
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGA
EST: gi|208369314|gb|DC955859.1|DC955859
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|100420708|gb|BY993475.1|BY993475
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTTA
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATT-A
EST: gi|162150909|gb|FC327389.1|FC327389
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|18335934|gb|BJ167955.1|BJ167955
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
EST: gi|208364180|gb|DC947284.1|DC947284
EST:     CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAG                         GCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT
genomic: CCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTAT

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: 24 (upstream exon), 33 (downstream exon)
Score: 12

CGATGCTTTTCGATTGATCAACCCTCAAACAATGATGTTGGGACAGGAGCCCAGACAAACCACATCGAACGTTGGACATCTTAACAAGCCCTCCATCCAGgttcttatgt ... tgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctctagatattaatgatattaacctacattaatggttgtaatgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA
          atattaatgatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgacgctgcagaggatgcagaatgtaagtgggttgcatcgtactattctctagatattaatgatattaacctacattaatggttgtaatgtttcacagGCTTTAATCCATGGATTAAACCGACACTACTATTCAATCGGAATTAATTATCGGAAGAATGAACTAGAAGAGAAAATGCTTTTGAACCTTCACAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - -cgctgca