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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S28_196V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os10g34180.1 (Oryza sativa), 5'ss of exon 3
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
||||||||  ||||  || | ||||| |||||||| || || ||||||||||||||||| ||| |||||||    || || || ||  | || || ||||||  |   || ||||||   | |   |    |   ||      ||  ||  ||   | |  |||    | ||  || |           ||  ||                                    
CAGAGCACTCTGAAAAGAGTAGGAGTAAACACCATCCCTGGCATTGAAGAGGTTAACATTTTCAAGGATGATGTGGTTATTCAGTTTCTGAATCCTAAAGgtgaga--tcacttgaatactaaaatgcaagttctacacgattagtaatc-tacttgctttcttatattttatttcttggttttg----ttccag------------------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g63400.1 (Oryza sativa), 5'ss of exon 3
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgct-tcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
||||||||  | ||| || | || || |||||||| ||||  || || ||||| ||||||||| |||||||   ||||||||| ||||| || |||||||||||      || |    |||   ||  |   || ||| ||| |  |   |       | | | | |||| ||| |    |     ||        |||||                               
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcatccctcctgttt---tgcctaccgt-accatggaaatgccaactgcttcttggtgttagat-tacttatccatgttcgat-ccgacctgtgcag-----------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G131577_T02 (Zea mays), 5'ss of exon 2
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatg-cattcc----cttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
||||||||| ||||  || | ||||||||||||||||| || ||||||||||| ||||||||  |||||||    || || || || || || || ||||||| |  | |||    |     | |  || || ||    |  ||||    |  || ||| | |    ||    ||| |  | | |                                                   
CAGAGCACCCTGAAAAGAATAGGAGTGAACACCATTCCTGGTATTGAAGAGGTCAACATCTTTAAGGATGATGTTGTTATTCAGTTTGTGAATCCTAAAGgtaagatactccagaccccagtactcaacaggatta---gtacttgacttattttctaacaatattttttt--tgttccccttcag--------------------------------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G001887_T03 (Zea mays), 5'ss of exon 3
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatt--tgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
|| |||||||||||  || | |||||||||| |||||| || ||||||||||| ||||||||  |||||||    || || || || || || || ||||||||| || | || ||      |            |     |        || ||||| |    |   | |   | |||                                                      
CAAAGCACCTTGAAAAGAATAGGAGTGAACAGCATTCCTGGTATTGAAGAGGTCAACATCTTTAAGGATGATGTTGTTATTCAGTTTGTAAATCCTAAAGgtatg-atactctggactccagtactcaacaagattagtacttcacttatttctaaaaatattttgtgggttcccctccag----------------------------------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G041881_T02 (Zea mays), 5'ss of exon 3
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
|||||||| |||||  || | ||||||||||| ||||| || ||||| ||||| ||||||||| |||||||    || ||||| |||   ||||| |||||||       || ||  |      |  || |              | |||||| ||||| |  | | ||   ||  ||| | |       |  ||                                    
CAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAGGTCAACATCTTCAAGGATGATATTGTTATCCAATTCCAGAACCCTAAAGgtaaatcccgccatgcgaacacgttacttct------------gcatattatagaagtt-gtctgacattatcaatctttctctgtttcctgcag------------------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EDO98665 (Chlamydomonas reinhardtii), 5'ss of exon 2
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaag--ttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
|| | |||| | ||||| || || ||||||||||| ||||| || || ||||||||||| ||| |||||||   |||||| |||||||| |||||||| |||  |          |     | | |        | || || ||| |         |  | ||  |||       ||  || | ||   ||                                          
CAAAACACCCTCAAGCGCCTGGGCGTGAACACCATCCCCGGCATCGAGGAGGTTAACATTTTCAAGGATGACAGCGTCATTCACTTCGTGAACCCCAAGGgtgggtccgaaaggaagcaggggcagcagcgcagggccgtgagagtgccagccgggggctccgtctcacggcactatgtttgctcctcgcag-----------------------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ08565 (Selaginella moellendorffii), 5'ss of exon 2
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
|||| |||  | ||| | || || |||||||||||||||||||| || || |||||||||||| |||| ||    ||  | ||||| || |  ||||||||| || |  |  ||    |    |   || ||      ||        ||| |   | |||   ||    | | |   | ||  |   ||||     |  |                              
CAGAACACGCTCAAGAGGCTGGGCGTGAACACCATTCCCGGAATCGAGGAAGTTAACATCTTCAAGGACGACATTGTTCTTCACTTTGTCAGTCCCAAAGgtttggaaccattttttttcctccattttcttccaggttttttttttcttagatccgatcgac-caacctttcttttcttcattacttattttcaccttgt------------------------------

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ19629 (Selaginella moellendorffii), 5'ss of exon 2
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgt-gaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag
|||| |||  | ||| | || || |||||||||||||||||||| || || |||||||||||| |||| ||    ||  | ||||| || |  ||||||||| || |  |  ||    |    |   || ||   | | ||        ||| |   | |||    |  | |   | |||        | ||| |   ||                                
CAGAACACGCTCAAGAGGCTGGGCGTGAACACCATTCCCGGAATCGAGGAAGTTAACATCTTCAAGGACGACATTGTTCTTCACTTTGTCAGTCCCAAAGgtttggaaccattttttttcctccattttcttccaggcttttttttttcttagatccgatcgaccaaccttttttttcttcattacttcttttcaccttg--------------------------------

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|67691830|gb|BJ952063.1|BJ952063
EST:     TCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: TCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67568857|gb|BJ941681.1|BJ941681
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|7583801|gb|AW699705.1|AW699705
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67508609|gb|BJ941471.1|BJ941471
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67575201|gb|BJ948025.1|BJ948025
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|37824378|gb|BJ582444.1|BJ582444
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67698660|gb|BJ958893.1|BJ958893
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67699536|gb|BJ959769.1|BJ959769
EST:     GTTANCCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|162244341|gb|FC423814.1|FC423814
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67576050|gb|BJ948874.1|BJ948874
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|162244340|gb|FC423813.1|FC423813
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|162201321|gb|FC376839.1|FC376839
EST:     GGTTAACATCTTCCAGGAGGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTTTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTTTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|18361165|gb|BJ193230.1|BJ193230
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|18345206|gb|BJ177247.1|BJ177247
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67696648|gb|BJ956881.1|BJ956881
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|162201322|gb|FC376840.1|FC376840
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67573263|gb|BJ946087.1|BJ946087
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|67692062|gb|BJ952295.1|BJ952295
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
EST: gi|37839056|gb|BJ597064.1|BJ597064
EST:     GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAG                         TGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA
genomic: GGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGA

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: 34 (upstream exon), 33 (downstream exon)
Score: 41

CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattc ... atgtgtgcagTGCAAGCCTCTATTGCTGCCAACACGTGGGTGGTGAGTGGACCTTCTCAGACGAAGAAGCTTCAAGATATCTTGCCCAGTATCATTAATCAGCTAGGACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgcttcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG