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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatatgtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG

Basic information

species Physcomitrella patens
transcript PP1S1_527V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 5
gtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatatgtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG
                                                 |   |   |     ||    |  |   | || | | ||   | ||||    |   |    ||||  |  ||   ||| |       |  | ||    || | |     || | | | ||| | ||||||||||||||||| ||||||||||| ||||| |||||||||||||||| ||||   || | ||| || ||| ||
------------------------------------------------gtatcactatatgattcctttatgccttgttgagttcag---tggctgcatcttttgttgttgtattggccatttcttttatgc---taatttggtg-gtttttacttttgaaattttcagCTTGGAGCCAATGCTATTTTGGCAGTGTCACTTGCTGTCTGCAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 5
gtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatat-gtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgt---attatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG
                                                          | |   |||    |   |  |||  |   || |   ||  ||       | | ||| |      |||       | || |  || |   |  | | ||| | |   | | | ||| | ||||| ||||||||||| ||||||||||| ||||| || ||||||||||||| ||||   || | ||| || ||| ||
----------------------------------------------------------gtatcactatgttttttgtttgtcttgttgagt--ttggtgactgcatcttttgtagccgtgttggccatccattttaag--ctaatcgggttttcacaatattgaaattttcagCTTGGAGCTAATGCTATTTTGGCAGTGTCACTTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 5
gtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatatgtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgc-agTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG-------------------
                                                                                                           || ||||  | |   |||| |  ||| | | ||   ||      || |  |   || | | ||||||| |||||||||||||| || |||||  |||| ||||||||||| || ||||| || |  ||||  ||  | ||||||                   
----------------------------------------------------------------------------------------------------------gta-gtaaaaaactttgcttttttctcga-gctcgctcatcctcttttcgtttctttgttctagTTGGGGGCCAATGCTATTTTGGCCGTGTCTTTGGCCGTGTGCAAGGCCGGAGCTGGCGTTTCCAAGATCCCTTTGTACCAGCACATTGCCAACCTTGCCG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ32861 (Selaginella moellendorffii), 3'ss of exon 5
gtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatatgtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgc-agTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG-------------------
                                                                                                           || ||||  | |   |||| |  ||| | | ||   ||      || |  |   || | | ||||||| |||||||||||||| || |||||  |||| ||||||||||| || ||||| || |  || |  ||  | |||| |                   
----------------------------------------------------------------------------------------------------------gta-gtaaaaaactttgcttttttctcga-gctcgctcatcctcttttcgtttctttgttctagTTGGGGGCCAATGCTATTTTGGCCGTGTCTTTGGCCGTGTGCAAGGCCGGAGCTGGCGTTTCCAAAATCCCTTTGTACCTGCACATTGCCAACCTTGCCG

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|67717547|gb|BJ967806.1|BJ967806
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100387077|gb|BY951476.1|BY951476
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|67717549|gb|BJ967808.1|BJ967808
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18365747|gb|BJ197824.1|BJ197824
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18370202|gb|BJ201804.1|BJ201804
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|208359629|gb|DC934616.1|DC934616
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18367870|gb|BJ199953.1|BJ199953
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGC
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGC
EST: gi|208357716|gb|DC902282.1|DC902282
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCANAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|208384682|gb|DC907127.1|DC907127
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18361801|gb|BJ193868.1|BJ193868
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100369601|gb|BY948562.1|BY948562
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100409225|gb|BY991908.1|BY991908
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100438709|gb|BY961762.1|BY961762
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|208394185|gb|DC933853.1|DC933853
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100428551|gb|BY977864.1|BY977864
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18365894|gb|BJ197972.1|BJ197972
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100365044|gb|BY966782.1|BY966782
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18366311|gb|BJ198390.1|BJ198390
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18365720|gb|BJ197797.1|BJ197797
EST:     TCATGAACTTGACGGTACCCAGAACGAGTGGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TCATGAACTTGACGGTACCCAGAACGAGTGGGGG-TGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18365449|gb|BJ197525.1|BJ197525
EST:     TCATGAACTTGACGGTACCCAGAACGAGTGGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TCATGAACTTGACGGTACCCAGAACGAGTGGGGG-TGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18366932|gb|BJ199012.1|BJ199012
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100448364|gb|CJ972663.1|CJ972663
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18374449|gb|BJ206027.1|BJ206027
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18371296|gb|BJ202898.1|BJ202898
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAA
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAA
EST: gi|208378006|gb|DC906935.1|DC906935
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100440922|gb|BY962410.1|BY962410
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100401183|gb|BY990872.1|BY990872
EST:     TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAG                         TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT

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: 32 (upstream exon), 31 (downstream exon)
Score: 6

GACCCTACAGATCAAACTGGAATTGACAACTTCATGGTTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatct ... tattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG
                                  atcttac  putative branch site (score: 6)
                                           tgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatatgtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgcagTTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA