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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggtttgaatttcgtgctcgacgatgg...

Basic information

species Physcomitrella patens
transcript PP1S67_176V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os01g11110.1 (Oryza sativa), 5'ss of exon 1
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGC--GTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggt-ttgaatttcgtgctcgacgatgg
    |  | | | ||   | | ||    |   | ||     |   |  | ||   ||  || |||||||||||||||||||||||||| ||||||||||| ||| || | ||      | ||  ||       | |    | |     |   | |  | ||   |  | |||  ||||| |||   |  |||   |    |||
--CAGCCTCGCTCAGCTCGATCTCTCTCTCGTCTCGCCATGGCCCCCAGCGACGACCTCGTCTACATGGCCAAGCTCGCCGAGCAGGCCGAGCGATACGACGgtacgcgatcccccccggctccctcctcccccctgccgttcctccctacctctgctcgtgcttgggggttttgtggtgttgtgctgtgtgtgtgttt-tgg

upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os11g39540.1 (Oryza sativa), 5'ss of exon 1
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcg--tgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggtttgaatttcgtgctcgacgatgg
                                      ||||||| | ||||    ||||    |||||||||||||||||||||||||| ||||||| |||  |  ||   | |     | || ||   |    || | |   |  || | ||| ||    |  | |   | |||  |||| |||| | | | |  |    
------------------------------------ATGAAGGAGAGGGAGAAGGTGGTGCGACTGGCCAAGCTCGCCGAGCAGGCGGAGAGATACGACGgtatggctgggatgggatctcggattgctggattgttcgattgcgcgtt-gctgttgtgcagttcttgttcttggttctttgcatttgggggttgggggga-

upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagag-actgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggtttgaatttcgtgctcgacgatgg-
    | || ||   ||| |       |  |     |  | ||||||| ||||  |  |||| | |||||||||| ||||||||||||||||| ||||| |||| | | ||| |      |   ||  |  |  |  |  |||          |    |      || | |   | |  |||   |  |||| |  |  |   
GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccgccgtacgggactacagtctctactctagcg--ttgttctcggtgcccttcagttca

upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA12G33800.3 (Glycine max), 5'ss of exon 1
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtg-cgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggtttgaattt-cgtgctcgacgatgg----
       |  ||| |           ||||    |    ||||| || |||| |   || ||||| |||||||||||||| ||||| ||||||||||| |||  |   |||||       |  ||  ||     ||||  ||     |    |||| |||   |  || || | || ||    |||    | | |    |      
CAAACCCTAATTTCGGAAAGATCGGCGATGGCTGCCTCCAAGGATCGCGAGAACTTCGTCTACATCGCCAAGCTCGCCGAACAGGCCGAGCGATACGAAGgtttcaaattcttcctttgttttctctga----ctttgacgcgcacatgcgcgtcgatgtgcgt--gattttgatgattcctttttatacggttgcttgtttctac

upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA02G12930.2 (Glycine max), 5'ss of exon 1
--TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggt----ggtttgaatt--tcgtgctcgacgatgg-
     | |||| | |      |||  |  |||  |   ||||| ||| | |||| |||||| ||| |||||||||| ||||||||||| ||| ||||||| |||       ||||  | ||| ||      |  |||| ||  | |||||  | |  ||  || ||    ||  ||    | |||||||   | ||  |  |  |||  
GTCGCTTTGTGATCTCT--CTCTGCAACCATGTCCGTCGAGAAAGAGAGAGAGACCCAGGTTTACTTGGCCAAGCTTGCCGAGCAGGCCGAGAGATACGAAGgt-------cttgttacacttacccttcttttttttctttttttttttaatctgatttctttttttgtttttgtttttgttttgaatgagttgttttttaaaatgtt

upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA01G07070.1 (Glycine max), 5'ss of exon 1
--TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagt-tcggtggtttgaatttcgtgctcgacgatgg--
     | |||| | |      |||  |  |||  | | ||||| ||| | |||| |||||| ||| |||||||||| ||||||||||| ||| ||||||| ||| | ||||      |  ||   |     | ||| |  |     |||| ||||  |||||| ||   || | | |  ||| ||| |  | || || |  |   
GTCGCTTTGTGATCTCT--CTCTGCAACCATGTCCGCCGAGAAAGAGAGAGAGACCCAGGTTTACTTGGCCAAGCTTGCCGAGCAGGCCGAGAGATACGAAGgt-cttgttacacttacgctttttttt--ttcttataatctgagtttttttgtttttgttttttaatgtgttgttttttttaatgtttttcttgatggggttt

upper sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 5'ss of exon 1
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgtt-gtttcttcgagttcggtggtttga--atttcgtgctcgacgatgg-
 |  || ||  |     |  ||  |  |||   || ||||||||  | ||||  ||||| |||||||||||||||||||| ||||| ||||| || || |||     || ||           | |      ||  |||| | || |||| ||  ||  || |||||  |  ||   ||||   | ||| ||   |     || 
GTGGGTTTGTCTCTCTTTCTTGCAACAATGTCGACCGAGAAGGAAAGAGAGACTCAGGTTTACATGGCCAAGCTCGCCGAACAGGCTGAGCGCTATGAAGgttttcttttttttcttttcctttaat----tttgggttgtttttcttgtcgttttttattgcttcggatctgggtttttggggaattcatgaatggatgcggt

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|162230671|gb|FC406094.1|FC406094
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162277839|gb|FC454302.1|FC454302
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162224456|gb|FC399832.1|FC399832
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162259102|gb|FC436409.1|FC436409
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|208360989|gb|DC957496.1|DC957496
EST:     AGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAAGTGGCGAAGCTTGATGTGGAGCTGACA
genomic: AGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAG-AAAGTGGCGAAGCTTGATGTGGAGCTGACA
EST: gi|208382964|gb|DC927714.1|DC927714
EST:     GGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162241145|gb|FC414163.1|FC414163
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|208356273|gb|DC957349.1|DC957349
EST:     GGTGTACATGGCCAAGCTCCCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|22492501|gb|BU052424.1|BU052424
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|67575498|gb|BJ948322.1|BJ948322
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|208365818|gb|DC951053.1|DC951053
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|208386680|gb|DC929126.1|DC929126
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162229445|gb|FC405831.1|FC405831
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162242248|gb|FC418448.1|FC418448
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162210235|gb|FC386421.1|FC386421
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|208366918|gb|DC951405.1|DC951405
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|162243339|gb|FC417040.1|FC417040
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
EST: gi|67575400|gb|BJ948224.1|BJ948224
EST:     GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATG                         AGATGGTGGAGTCGATGAANAAAGTGGCGAAGCTTGATGTGGAGCTGACAG
genomic: GAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAG

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: 33 (upstream exon), 34 (downstream exon)
Score: 93

TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttc ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGATGTGGAGCTGACAGTAGAGGAGCGAAATCTCTTGTCTGTGGGTTACAAGAATGTGATTGGTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagagactgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggtttgaatttcgtgctcgacgatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG