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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccatttctaaccgcccactgtcaacagcaaatttgcgagcttcttagtacagggattccatatgatttccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG

Basic information

species Physcomitrella patens
transcript PP1S5_30V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 2
gtacccatttctaaccgcccactgtcaacagcaaatt-tgcgagcttcttagt---acagggattccatatgatttccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG
                       ||    |  | ||| | |  |   ||| ||   | | | || | |||  ||  || | | |     ||  ||||        |  |||  ||   |||   |||||||| || |||||||| ||||| |||||||||||| ||||||| ||| ||    | ||  | |||
-----------------------gtatgtaatatattctacatggcactttgttggatatgaatacgataatatg-ccaaataagaatggttattaat-------attgttgttg--tatcacattgcagTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCTCTAGGGCTTCAG

upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 10
gtacccatttctaaccgcccactgtcaacagcaaatttgcgagcttcttagtacagggattccatatgatttccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG
                          || |    |  ||  |  || || | | | | ||   |||  ||  || | | |     ||  ||||        |  |||  ||   |||   |||||||| || |||||||| ||||| |||||||||||| ||||||| ||| ||    | ||  | |||
--------------------gtatgtaatattctacatggcactttgttgg-atatgaatatgataatatg-ccaaataagaatggttattaat-------actgttgttg--tatcacattgcagTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCTCTAGGGCTTCAG

upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 10
gtacccatttctaaccgcccactgt-caacagcaaatttgcga-gcttcttagtacagggattccatatgatttccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG
                    | | |  || |     ||   ||   ||  | | | | | ||   |||  || ||  ||  |    | || |||              | || || |||   |||||||| || |||||||| ||||| |||||||||||| ||||||| ||| ||    | ||  | || 
--------------------agtatgtaatatattcttcatgacattttgttggatatgaatatgataatatgtcaaataaa----aatggttattaatgttg-----ttgttaa-atcacattgcaGTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCTCTAGGGCTTCA-

upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacccatttctaaccgcccactgtcaacagcaaatttgcgagcttcttagtacagggattccatatgatttccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG-------------------------------------
                             |     || || | | | |||     |    |   |  | | || | | || |    | ||    |       |  || ||||  ||      ||||||||| || || || || ||||||||||||||| ||||||||||| |   | | ||  | |||                                     
---------------------------gtactcttttggcaaaccttttat----gttgcttttttcgttatctgttgtaatatgctcttgcttcatgttgtacctttgtgataat------gcagTTAGGAATAGCCATTGTTAACGACTTCAAAAGTGTTGAAGGAGATAGAGCATTAGGACTTCAGTCTCTCCCAGTAGCTTTTGGCACCGAAACTGCAAAAT

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|162165040|gb|FC342231.1|FC342231
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|162232905|gb|FC407532.1|FC407532
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|67698756|gb|BJ958989.1|BJ958989
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|208347302|gb|DC917177.1|DC917177
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|162232906|gb|FC407533.1|FC407533
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|162163835|gb|FC340057.1|FC340057
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|37831959|gb|BJ589971.1|BJ589971
EST:     TCTATCATGGGACGTCGTTATTCTTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: TCTATCATGGGACGTCGTTATTC-TTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|162165041|gb|FC342232.1|FC342232
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
EST: gi|208365422|gb|DC950889.1|DC950889
EST:     CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGG                         TTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA
genomic: CTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAA

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: 30 (upstream exon), 31 (downstream exon)
Score: 5

GTGGGCGGGACAAGCATTGTTCGGTACTCTATCATGGGACGTCGTTATTCTTACTCTTTTGTACAGTACTGCTGGGgtacccattt ... ccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG
                gtttaac  putative branch site (score: 5)
                                          catcctttt  putative PPT
     tttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccatttctaaccgcccactgtcaacagcaaatttgcgagcttcttagtacagggattccatatgatttccgatttattgcagtgtttaaccggacgaaaggttcgtgaacatccttttgcagTTAGGGATTGCTATCGTCAACGACTTCAAAAGTATTGAAGGAGATCGGCAAATGGGTTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC