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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG

Basic information

species Physcomitrella patens
transcript PP1S79_253V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
-----------agcaatagtttctagtgtggcagctgtggccccagggact----ggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggt-tttgtag----cagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
             |     |||| |  |   ||   |  | | |   || |    | | ||  | ||| ||    | |  ||   ||   |  ||| |  || || |||| ||    | ||  ||||||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     | |       
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA-------

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
agcaatagtttc-tagtgtggcagctgtggccccagggactggtgttgttgttcct--ctgtcggt----gtcttgattga-ctgatttttctgtggttttgtag----cagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
 | ||   |     | |  |   | | ||  || |     || |||||||  || |  | |||  |     ||    ||   |||| |   || | ||||    |    | |   ||||||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     |         
-gtaactctccggcactccgctcgatctgttcctactagatg-tgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG--------

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1
agcaatagtttc-tagtgtggcagctgtggccccagggactggtgttgttgt-tcctctgtcggtgtcttgattgactgatttt--tctgtggttttgtagcagGTA--------AGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
 | |||  |     |    |   | | |   || |     ||   || | || | | | |||          |  ||| | | |  |  |   |||  | ||||| |        | ||||| ||||| ||||||||||| |||||||||||||| | ||||   |||||||| || || |||||    |||   ||     |         
-gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG--------

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
                        ||||      |        ||       || ||     |    |||||  |   ||| |  |  |   |   | ||   | ||||| ||||| ||||||||||| |||||||||||||| | ||||   |||||||| || || |||||    |||   ||     |         
-----------------------gtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgc-actttgttggcagGCATCCGGAAG---AAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG--------

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1
----agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
      |  | | |   |   |    | ||||      |        ||       || ||     |    |||||  |   ||| |  |  |   |   | ||   | ||||| ||||| ||||||||||| |||||||||||||| | ||||   |||||||| || || |||||    |||   ||     |         
gcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgc-actttgttggcagGCATCCGGAAG---AAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG--------

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G068496_T02 (Zea mays), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattga----ctgatttttctgtggttttgtagcagGTA----AGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
     ||  | || || |  |  | | | || |     | ||  | | ||||| |||   | | | ||| | ||    | | |   |  | |   | |    ||| |     |||||| ||||| ||||||||||| ||||| |||||||| | ||||   |||||||| || ||||||||                           
----gta-ctcctcgtcttcctcccgagtcctcct---ccggattcgatgttcgtctcctgatttattggtggaaccgcagGTGACTAGGAGCAGTAGCGAGAGGGATTCTGGATGGCCAAGTCGAAGAACCACACGGCGCATAACCAGTCGTTCAAGGCGCACAAGAACGGCATCAAGAA---------------------------

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G37060.1 (Glycine max), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---
              ||  |     |       |    ||    ||| ||  |  | ||  | | |||| |||| || |  ||       ||   | ||||   ||||||| ||||| ||||||||||| || ||||||||||||||||||  |||||||||||| ||||| |||   |||| |||     |||  || |    
--------------gttcgctctgttcaatttctctaac--acgttcttacttttttgctgctctcttcattgtcttacattgtgtgcattgaattgcag-

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---
                  |   ||| ||  |  |    ||    ||||| |  || ||| | | || |  |    |  |     | ||    |  |   |   ||||||| ||||| ||||||||||| || ||||||||||||||||||  ||| |||||||| ||||| |||   |||| ||||    |||  || |    
------------------gttcgctctgtgcaaattctctaac-ttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactg-gtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---
     ||  ||| | |   | | |     |  |      || |  ||||| |     |  |  | || |  |    | ||||| || |  |||| | ||||   ||||||| ||||| ||||| ||||| |||||||| ||||||||||||  |||||| || || ||||||||    |||| ||||    |||  || |    
gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctcta-ttttattgcag-

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtctt--gattgac---tgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---
     |   ||| | |   |   |        |    | |  ||| | | ||  |||||   | ||||   || | |   | |||||| ||    ||  | ||||   ||||||| ||||| ||||| ||||| || ||||| ||||||||||||  |||||| || || ||||||||    |||| ||||    |||  || |    
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgt-gctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcag-

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG-
              ||   ||  |||   |    || |     |  |  |||  | ||      |||   |  | |  |     |    |  |||||      | ||||||||||| |||||||||||||| |||||||||||||||||   |||||||||||| ||||||||       |||||     ||| ||| |  
--------------gtacagcctctgcatcttttggtaa-aacgacgccgtt--tttgctcccatctcactgaattcttccactttcaatgctgtagGG----AAATGGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACC

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|67693178|gb|BJ953411.1|BJ953411
EST:     GAGTCGCNTCGTCTGCGTCTTAG                         GTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
genomic: GAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... tttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
EST: gi|7584238|gb|AW700135.1|AW700135
EST:     ATTGTTTGAGTCGCCTCGTCTGCGTCTTAG                         GTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
genomic: ATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... tttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
EST: gi|67696537|gb|BJ956770.1|BJ956770
EST:     TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGCAG                       
genomic: TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTT---AGgtgcgttgtt ... tttgtagc
EST: gi|162268442|gb|FC444315.1|FC444315
EST:     ATATTGTTTGAGTCGCCTCGTCTGCGTCTTAG                         GTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
genomic: ATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... tttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
EST: gi|67573153|gb|BJ945977.1|BJ945977
EST:     ATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGCAG                       
genomic: ATATTGTTTGAGTCGCCTCGTCTGCGTCTT---AGgtgcgttgtt ... tttgtagc
EST: gi|67508207|gb|BJ941078.1|BJ941078
EST:     ATATTGGTTTGAGTCGCCTCGTCTGCGTCTTAG                         GTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
genomic: ATATT-GTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... tttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
EST: gi|67691427|gb|BJ951660.1|BJ951660
EST:     TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAG                         GTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA
genomic: TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... tttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGA

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: 10

CCTTTTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... tttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG
                           gactgat  putative branch site (score: 10)
                              tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC