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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGGAAGGAGTTTGATAAGACAGAGGACGACCTCAAGGCGTTGCAAAGTGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttttttattttgttcttgggctccctttcgcgttgctgtttacctggactggacgcctttggaccactgggatcgtaaggctggcagaggttg...

Basic information

species Physcomitrella patens
transcript PP1S91_182V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ13668 (Selaginella moellendorffii), 5'ss of exon 2
GCGAGGAAGGAGTTTGATAAGACAGAGGACGACCTCAAGGCGTTGCAAAGTGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttttttattttgttcttgggctccctttcgcgttgctgtttacctggactggacgcctttggaccactgggatcgtaaggctggcagaggttg
 ||| |||||||||||| ||||| ||||| || |||||||||||||| || || ||||| || || || |||||  |||| ||||| ||   ||||||||||||||  ||    |    | || |       | |  ||||     ||  ||    | |   ||||||   |  | |                       
TCGAAGAAGGAGTTTGAGAAGACCGAGGATGATCTCAAGGCGTTGCAGAGCGTCGGGCAGATTATAGGCGAAGTGCTGAGGCAGCTCGACAATGAACGCTgtgagtgcttggcttggcatcctcgtttgtgatctaacgttttctcttttctctttttgcttcctttg--tctgtag-----------------------

upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 2
GCGAGGAAGGAGTTTGATAAGACAGAGGACGACCTCAAGGCGTTGCAAAGTGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttttttattttgttcttgggctccctttcgcgttgctgtttacctggactgg-acgcctttggaccactgggatcgtaaggctggcagaggttg
 ||| |||||||||||| ||||| |||||||| |||||||||||||| || || ||||| || || || |||||  |||| ||||| ||   ||||||||||||||  ||    |    | || |       | |  |||| || ||  |      ||  ||   | || |                              
TCGAAGAAGGAGTTTGAGAAGACCGAGGACGATCTCAAGGCGTTGCAGAGCGTCGGGCAGATTATAGGCGAAGTGCTGAGGCAGCTCGACAATGAACGCTgtgagtacttggcttggcatcctcgtttgtgatctaacgtttctcttctctctttttgctacttgtctgtag-----------------------------
















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|67572554|gb|BJ945378.1|BJ945378
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100386933|gb|BY988202.1|BY988202
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100449435|gb|CJ973734.1|CJ973734
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100448214|gb|CJ972513.1|CJ972513
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|67508474|gb|BJ941340.1|BJ941340
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100378570|gb|BY968666.1|BY968666
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100426731|gb|BY977333.1|BY977333
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100403562|gb|BY954988.1|BY954988
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|100442911|gb|BY963406.1|BY963406
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
EST: gi|67703931|gb|BJ964164.1|BJ964164
EST:     TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCT                         TGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA
genomic: TGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACA

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: 35 (upstream exon), 32 (downstream exon)
Score: 15

GCGAGGAAGGAGTTTGATAAGACAGAGGACGACCTCAAGGCGTTGCAAAGTGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttt ... gtacgggcagTGATTGTCAAGGCAAGCAGTGGACCGCGATATGTGGTTGGATGCCGCAACAAGGTTGACAAAGAGAAGTTGATGGCTGGTACTCGAGTTGCATTGGATAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGGAAGGAGTTTGATAAGACAGAGGACGACCTCAAGGCGTTGCAAAGTGTGGGGCAAATCATCGGAGAAGTCTTGAGACAGCTTGATTCTGAACGCTgtgagttttttttattttgttcttgggctccctttcgcgttgctgtttacctggactggacgcctttggaccactgggatcgtaaggctggcagaggttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT