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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgtggcggacaaacattactgtgcttgaaaaggaagtactgccaaaacatgttgcgatagtgataacagtaatgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG

Basic information

species Physcomitrella patens
transcript PP1S24_182V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S24_182V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g37160.1 (Oryza sativa), 3'ss of exon 1
--------tgtttgtg-gcggacaaacattactgtgcttgaaaaggaagtactgccaaaacatgttgcgatagtgataacagtaatgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG
        |||||||| |    |   ||||| | |||    | || |  || |        |  ||    |    |   |||  |    ||| |     ||||   |||| ||||||  ||||||| || || |||||  |  | || ||||||||||||||||||||||| ||||| | ||| ||||||||||  ||  ||  |||| 
atgctttatgtttgtgcgattcccctcattattctgcactgacagcagctattttgttgctaatttattttga-aaggtcagctaaccattcaa-----tttg---cagGATGATGAGCTTCAAGTTAAAGTCAACAAGCTTTCGTCTACGAAGACACAACTTCCATATGACTACTATTTTCTAGACTACTGCAAACCTGAGGCAATTA

upper sequence: PP1S24_182V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 1
tgtttgtggcggacaaacattactgtgcttgaaaaggaagtactgccaaaacatgttgcgatagtgataacagtaa-tgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG
|  |  |  |         || |||   ||     |    || |         ||||   | | |||  | | | | | |||       |  | | | ||||||||     |    || || |||||||| ||| ||||||| ||||| |||||||||||||| |||||||   |  | || ||||  || || || ||  
ttatcatttcaatttgtttttgctgctgttatttggtttttaattgtgtg-tgtgtttgaagaatgaagatattgagttattgtttcatgtgtggcaccagGGTGACCCCCTCTCTGTCAAAGTGAACAAGTTATCATCCACCAAGACTCAACTTCCATATGACTACTACTTCTTGAAGTATTGCAAACCCAAAAAGATAT

upper sequence: PP1S24_182V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 1
tgtttgtggcggacaaacattactgtgcttgaaaaggaagtactgccaaaacatgttgcgatagtgataacagtaa-tgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG
  ||| |     | |    ||   |   |||         | ||         ||||   | | |||  | | | | | |||       |  | | | ||||||||     |    || || |||||||| ||| |||| || ||||| |||||||||||||| |||||||   |  | || ||||  || || |  ||  
attttattattta-attttttttcgctgttgttttttgctttctaattttgtgtgtttgaagattgaagatattgagttattgtttcatgtgtggcaccagGGTGACCCCCTCTTTGTCAAAGTGAACAAGTTATCATCTACCAAGACTCAACTTCCATATGACTACTACTTCTTGAAGTATTGCAAACCCAAAACGATAT

upper sequence: PP1S24_182V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
tgtttgtggcggacaaacattactgtgcttgaaaaggaagtactgc---caaaacatgttgcgatagtgataacagtaatgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG
| | | ||       |  | |   |    | |||    | |  |         |    |  || || |  | |  |  |  |||||   |  | ||    ||||| |||    |  | ||||||||||||||| |||| || || |||||||||||||| ||    ||||| ||||||   || |||   ||  | |  || |
tatatatgttatgatattacttgagatactaaaaccttattcttatgtttgtgatggatcacggtatt--tgattgcta-aatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG

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|100422504|gb|BY976406.1|BY976406
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|18325719|gb|BJ157716.1|BJ157716
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|208350408|gb|DC906110.1|DC906110
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|18344133|gb|BJ176172.1|BJ176172
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|18328604|gb|BJ160609.1|BJ160609
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|18362477|gb|BJ194547.1|BJ194547
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|18325392|gb|BJ157388.1|BJ157388
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|162256884|gb|FC432986.1|FC432986
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|100405258|gb|BY955435.1|BY955435
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACGA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|67704072|gb|BJ964305.1|BJ964305
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|208352204|gb|DC906307.1|DC906307
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAANGTGAACAAATTAACATCCACGAANACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
EST: gi|18362890|gb|BJ194962.1|BJ194962
EST:     TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAG                         GGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA
genomic: TCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAA

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: 25 (upstream exon), 11 (downstream exon)
Score: 1

CGCTTGCGCTGCCTTCATGCTGCTCGTGTCGGTCTTGCCGGTTGTGCCGCTCGCATCTGGGTTCTACTTGCCTGGCGTGGCGCCCCTGGACCTTGCTCAGgtatgtgtgt ... tttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaaacatgttgcgatagtgataacagtaatgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG
                   tgataac  putative branch site (score: 1)
                            taatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgtggcggacaaacattactgtgcttgaaaaggaagtactgccaaaacatgttgcgatagtgataacagtaatgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA