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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGGGCCACTGTGGATCATGCTGGGCTTTTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatcaacttgaagtctattttaactgtgatacacatatgcaatgattttacattcatcttcattttggggtgtttcgatcggagactggcacattgctggctgaatcctcttggacataaagttcatgtaatctcgacctggtttaagtgaatgggggttgatagagtttgaattttcggtgttggtgaatcag

Basic information

species Physcomitrella patens
transcript PP1S79_128V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_128V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ32889 (Selaginella moellendorffii), 5'ss of exon 5
ATCAGGGCCACTGTGGATCATGCTGGGCTTTTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatcaacttgaagtctattttaactgtgatacacatatgcaatgattttacattcatcttcattttggggtgtttcgatcggagactggcacattgctggctgaatcctcttggacataaagttcatgtaatctcgacctggtttaagtgaatgggggttgatagagtttgaattttcggtgttggtgaatcag
     || |||||||| |||||||||||||||||||| |  ||  || |||| ||||| || ||||| | ||  ||||| || |||    ||  |    ||| ||||    ||| | ||       |  |||  | |  |  |||                                                                                                                                       
-----GGTCACTGTGGGTCATGCTGGGCTTTTGGAGCTGTCGAGGCACTGACGGATCGATTTTGCATCCTCAACAATGAAgtgagtggagaatctt--ttcttttttgttcgtg-tgcattgtgatacagatgcttcgcttttctcag------------------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S79_128V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ05715 (Selaginella moellendorffii), 5'ss of exon 5
ATCAGGGCCACTGTGGATCATGCTGGGCTTTTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatcaacttgaagtctattttaactgtgatacacatatgcaatgattttacattcatcttcattttggggtgtttcgatcggagactggcacattgctggctgaatcctcttggacataaagttcatgtaatctcgacctggtttaagtgaatgggggttgatagagtttgaattttcggtgttggtgaatcag
     || |||||||| |||||||||||||||||||| |  ||  || |||| ||||| || ||||| | ||  ||||| || |||    ||  |    ||| | |     ||| | ||      ||  |||  | |  |  |||                                                                                                                                       
-----GGTCACTGTGGGTCATGCTGGGCTTTTGGAGCTGTCGAGGCACTGACAGATCGATTTTGCATCCTCAACAATGAAgtgagtggagaatctt--ttctttctcgttcgtg-tgcattgtgacacagatgcttcgcttttctcag------------------------------------------------------------------------------------------------------------------------------------
















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|100385275|gb|BY950867.1|BY950867
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|100394861|gb|BY989962.1|BY989962
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|18331434|gb|BJ163445.1|BJ163445
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|100396641|gb|BY990226.1|BY990226
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|100383576|gb|BY950360.1|BY950360
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|100369727|gb|BY967362.1|BY967362
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGNCG-ATTTGAGTG
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTG-CGGATTTGAGTG
EST: gi|100383471|gb|BY950255.1|BY950255
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|100382602|gb|BY986877.1|BY986877
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|208371635|gb|DC932464.1|DC932464
EST:     TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
EST: gi|208363376|gb|DC946974.1|DC946974
EST:     TTGGAGCAGCGGAATCATTGANTGATCGCTTNTGCATTCACATGAATGAG                         AGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT
genomic: TTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGT

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: 27 (upstream exon), 28 (downstream exon)
Score: 2

ATCAGGGCCACTGTGGATCATGCTGGGCTTTTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatc ... ggtgaatcagAGTGTGTCACTATCAGAGAACGATCTCCTAGCCTGCTGCGGATTTGAGTGTGGCGATGGTTGTGACGGTGGGTACCCCATCAGAGCCTGGCGATACTTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAGGGCCACTGTGGATCATGCTGGGCTTTTGGAGCAGCGGAATCATTGACTGATCGCTTCTGCATTCACATGAATGAGgtaagtaatcaacttgaagtctattttaactgtgatacacatatgcaatgattttacattcatcttcattttggggtgtttcgatcggagactggcacattgctggctgaatcctcttggacataaagttcatgtaatctcgacctggtttaagtgaatgggggttgatagagtttgaattttcggtgttggtgaatcag

- - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - -  GAGCAG