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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacttgtttatttgtttaagtcctgtttcttcttatttttatttgtttatcttgttgttgtggattggttaaatctttgaggcttcataatgtatcagcttgttattttttgaaacattccagttgcatgtcaggtattgattttgttgatgaatgcttatttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGCCAGCAGTGCAAGATGGTTGTTCAGCAGTATGGTGACCAGATTGTTGAGA

Basic information

species Physcomitrella patens
transcript PP1S93_73V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S93_73V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G62290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtgagaacttgtttatttgtttaagtcctgtttcttcttatttttatttgtttatcttgttgttgtggattggttaaatctttgaggcttcataatgtatcagcttgttattttttgaaacattccagttgcatgtcaggtattgattttgttgatgaatgcttatttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGCCAGCAGTGCAAGATGGTTGTTCAGCAGTATGGTGACCAGATTGTTGAGA
                                                                     |  |  ||  |   |||  || |||  || | |  |   |   |||    | ||     ||||   | | ||  | |||||  || | | | |||     | ||||   | |||||    || ||  |||| ||||| ||  |||| ||||||||||||||||||||||  |||||| | ||||||||  |    ||| | ||  
--------------------------------------------------------------------gtaagcaaataccacgag--tttata--gttttatttcagttagtttgagtatatgt---ttgctcttgaagttctcattttcctggtaatttctt-----tctagGCTGTGGTTGCCATGATAAATAAGGCTATTGGAGCATCTGGAGTTGTTAGCCAGCAGTGCAAGACTGTTGTTGACCAGTATGGACAAACCATTTTGGATT
















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|162227601|gb|FC402308.1|FC402308
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|162187793|gb|FC364172.1|FC364172
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|100356155|gb|BY946224.1|BY946224
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|208362837|gb|DC950637.1|DC950637
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|161982347|gb|EE296254.1|EE296254
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|162162646|gb|FC338948.1|FC338948
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|162180470|gb|FC356112.1|FC356112
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|208375136|gb|DC944861.1|DC944861
EST:     TGCTNGACCATCG                         GGAATCG-TGCAG-AATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: TGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
EST: gi|162164608|gb|FC341903.1|FC341903
EST:     GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCG                         GGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC
genomic: GTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGC

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), 35 (downstream exon)
Score: 129

TCTTGGTGATGTAACCATCAATGGACGCACCACAGGTTTCTGTGCGAATGGTTGCACTGCCATTGCTGATTCCGGCACGTCGCTGCTTGCTGGACCATCGgtgagaactt ... atttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGCCAGCAGTGCAAGATGGTTGTTCAGCAGTATGGTGACCAGATTGTTGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattccagttgcatgtcaggtattgattttgttgatgaatgcttatttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGCCAGCAGTGCAAGATGGTTGTTCAGCAGTATGGTGACCAGATTGTTGAGA
                                          cttatttct  CT-rich tract
                     tattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacttgtttatttgtttaagtcctgtttcttcttatttttatttgtttatcttgttgttgtggattggttaaatctttgaggcttcataatgtatcagcttgttattttttgaaacattccagttgcatgtcaggtattgattttgttgatgaatgcttatttctgtagGGAATCGTTGCAGAAATCAACCAGGCCATTGGTGCTACTGGTGTTGTTAGCCAGCAGTGCAAGATGGTTGTTCAGCAGTATGGTGACCAGATTGTTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG