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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttttaacctacaatacattttgtgtgaaattattccactgacctcagtagctttataacttgatttactccttttgtcatattagatagtatg...

Basic information

species Physcomitrella patens
transcript PP1S64_201V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S64_201V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G437119_T02 (Zea mays), 5'ss of exon 11
CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaag------------ctttttaacctacaatacattttgt-------gtgaaattattccact------gacctcagtagctttataacttgatttactccttt-tgtcatattagatagtatg
 |||| |||||||||||||||||||| ||||| ||||||||| | ||||| ||||| ||||| |||||  | || |||||  | || || ||  |||||||||||             | ||| |   | |  ||   | ||       | ||||  ||||   |        | || | ||  || || ||  ||| ||| || | || | | || |  ||    
AGACAAATGACCTACAAGTTCCTCAACACTATAATTGATGACCTTTTTGCATTCGTCATTAAAATGCCAATGCTTCATCGTCTCTCGGTTTTCAGAGATGgtaagatgatctatcacttcttttagtcaaataactgctagttacagcagggaaaccattctgttcttttaatcttccgcaggcttctatct-aattgactgctctctgacgtgtttggcag----

upper sequence: PP1S64_201V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G016894_T01 (Zea mays), 5'ss of exon 10
CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttttaacctacaatacattttgtgtgaaattatt-ccactgacctcag------tagctttataacttgatttactccttttgtc---atattagatagtatg---------------------
 |||| |||||||||||||||||||| ||||| || |||||| | ||||| || || || || |||||  | || |||||  | || || ||  ||||||||||| |     | |||  |    ||||  || | || | | |   | |  ||||       |   |  |   | ||  |||   | ||||    ||     |  |  ||                     
AGACAAATGACCTACAAGTTCCTCAACACTATAATCGATGACCTTTTTGCATTTGTCATCAAAATGCCAATGCTTCATCGTCTCTCAGTTTTCAGAGATGgtaagat----gatctatcacttctttttagtcagataactgctggttaaatcagggaaaccattctgctctttggacataccattcttgtttagatccctaaccgactgctctctgacatgtctcggcag

upper sequence: PP1S64_201V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv07s0130g00170.t01 (Vitis vinifera), 5'ss of exon 11
CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctt---tttaacctacaatacattttgtgtgaaattattccactgacctcagtagctttataacttgatttactccttttgtcatattagatagtatg-
 | |||||||| ||||||||||||||||| ||||| |||||  | |||||||| || || || |||||  | ||||||||  | ||||| || || |||||| || |    |  ||  | || |  ||||| ||     ||||| |   |   ||| | |||||    |     || ||   |  |   |     |||  |   
AGGCAGATGACGTACAAGTTCCTCAATACCATCATAGATGATCTGTTTGCCTTTGTCATAAAAATGCCAGTGCTACATCGGCTTTCTGTGTTCCGTGATGgtgagttccaatcaaaattccactgtattttttgc----ttattgctgagttttcatttgctttgattcccatgttcctaaatgaggggttagcaatatcacat

upper sequence: PP1S64_201V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EDP02622 (Chlamydomonas reinhardtii), 5'ss of exon 15
--------------------CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttttaacctacaatacattttgtgtgaaattattccactgacctcagt--agctttataacttgatttactccttttgtcatattagatagtatg
                    || |||||||| |||||||||||||| || || || || ||| | || || |||||||||||||||||||| || ||  | | | ||         | |    |||     |     || |       | ||||   ||     |||  | | ||  ||           |   ||| | |                     
CCGTGGCGCACCTTCCCTGGCGCCAGATGACTTACAAGTTCCTCAACACCATTATCGACGACCTGTTCGCGTTCGTTATTAAGATGCCTCTGCTGCACAGgtgggctaacggaatcgttctcgagccacgca-tgggcattgataccagggtgatggtaggatgctgtacccggttgaggggcccgcaccggcctacgcat---------------------

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|37828146|gb|BJ586158.1|BJ586158
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|37839388|gb|BJ597396.1|BJ597396
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|67727249|gb|BJ977508.1|BJ977508
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|15728118|gb|BI740628.1|BI740628
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|37828863|gb|BJ586875.1|BJ586875
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|37842809|gb|BJ600817.1|BJ600817
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTNGTCTGTATTTCGAGATG                         ATATCGTTTTTCTNGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|162178560|gb|FC355012.1|FC355012
EST:     CTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTNGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|162158902|gb|FC334788.1|FC334788
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|208365740|gb|DC944168.1|DC944168
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCCTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|7584130|gb|AW700027.1|AW700027
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|162178561|gb|FC355013.1|FC355013
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|37846389|gb|BJ604397.1|BJ604397
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
EST: gi|162210480|gb|FC386776.1|FC386776
EST:     CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATG                         ATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA
genomic: CTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACA

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: 13 (upstream exon), 32 (downstream exon)
Score: 10

CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttt ... atacctgcagATATCGTTTTTCTTGTCTACTTGTATCAGCGTTGGAAGTATCCAGTTGACAAGAAGCGCGTCAATGAGTTCGGGTTTGGTGGAGATGATGAGAAGGAGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACAGATGACCTACAAGTTCCTCAATACTATCATTGATGACTTATTTGCCTTCGTTATTAAGATGCCTCTTCTACATCGCTTGTCTGTATTTCGAGATGgtaagctttttaacctacaatacattttgtgtgaaattattccactgacctcagtagctttataacttgatttactccttttgtcatattagatagtatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG