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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggcagttcactctcagaattttaggatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt...

Basic information

species Physcomitrella patens
transcript PP1S22_326V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagca------tgggcagttcactctcagaattttagg-at---gtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt------------------------------------------------------------------------------
                                | ||| |  | |||||| | || || |||||||| || ||||||||||||||||| ||||||||||||||||  ||   | |    |  |||| | |||      || |   ||  |||||   |||  |   ||   || || | | |  ||     ||| ||      | | |                                                                                 
CAAGAAGGGTAAGGACAGCCTGTCTGCCCAGGGAAAGCGCCGTTATGACCGTAAGCAGTCAGGATATGGTGGTCAGACCAAGCCTGTTTTCCACAAGAAGgtattgtg-acagtttatatgtgattacgcagtgctgtgtgtgattgtctctcttcattagaaacatatggtgtcatgatttgtgtctgttcaatgcaaacatgtggcaataaccatcatgtagttttaatgtatctgactttcagctgtgcatttttcatgttatgatacatggttcctgttttcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgg--gcagttcactctcagaattttagg---atgtctcgtcaatcctgctatctcagtgtt-tgtgtttcgtgt
                                | ||| |  | |||||| | || || |||||||| || ||||||||||||||||| |||||||||||||||   ||   | |    |  |||| | |||  |  |    | |||||| |    ||||    || |   ||||    || | | |||||| | ||||| |     
CAAGAAGGGTAAGGACAGCCTGTCTGCCCAGGGAAAGCGCCGTTATGACCGTAAGCAGTCAGGATATGGTGGTCAGACCAAGCCTGTTTTCCACAAGAAGgtactgtg-acagtttatatatgattatgcagtgttgtgtgtgactctctgttcattagaaacatatggtgtcatgattgatgtatcagtgctatgtgtct-----

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgg--gcagttcactctcagaattttagga---tgtctcgtcaatcctgctatctcagtg-tttgtgtttcgtgt---------------------------------------------------------------------------------------------
                                | ||| |  | |||||| | || || |||||||| || ||||||||||||||||| |||||||||||||||   ||   | |    |  |||| | |||  |  |    | |||||| |    |||| |   |     ||||    || | |  ||||| | ||||| | ||                                                                                               
CAAGAAGGGTAAGGACAGCCTGTCTGCCCAGGGAAAGCGCCGTTATGACCGAAAGCAGTCAGGATATGGTGGTCAGACCAAGCCTGTTTTCCACAAGAAGgtactgtg-acagtttatatatgattatgcagtgttgtgtgtgactctctgttcattagaaacgtacggtgtcatgattgatgtagcagtgatatgtgtct-gtacaatgcatgtggcaataaccatcacgtagttttaattgcatgtggctttcagctgtgcatttttcatgttatgatacatggttcctgttttcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G125527_T02 (Zea mays), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggcagttcactctcagaattttag----gatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt--------------------------------------------
                                | ||| |  | |||||| | || || |||||||| || |||||||||||||||||||||||||||||||||   |||   ||    |  ||||    | |   |  ||  || |    ||  |||     ||||||    |   |||| |  ||    |   ||||  |||                                             
TAAGAAGGGCAAGGATAGCCTGTCTGCCCAGGGAAAGCGCCGTTATGACCGCAAGCAGTCAGGATATGGTGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtaa--tgcagcatatctatttgattgtacttatacctttgtctgttttgatgctagcatgaatgtctgaaaatatctgcgaattctaaatgcctgttcagtgattaatgtgggatatgacaaatgagattgtatttatacctttcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G009412_T01 (Zea mays), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgta-tgttgcgta-------------atcagcacctgatgaagcatgggcagttcactctcagaattttaggatgt----ctcgtcaatcctgctatctcagtgtttgtgtttcgtgt-----------------------------------
                                | ||| |  | |||||| | || || |||||||| || || |||||||||||||||||||||||||||||| ||  |  ||             |  |   |   || || | |      ||  |  |    ||  ||| |||     ||    |   || | || ||    | | ||||  |||                                    
CAAGAAGGGTAAGGATAGCCTGTCTGCCCAGGGAAAGCGCCGTTATGACCGCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccatttctaaatgtctgttgggtgcacagattgggatatgacaaatgttgtgattttcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G103059_T01 (Zea mays), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggcagttcactctcagaattttag----gatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt--------------------------------------------
                                | ||| |  | |||||| | || || |||||| | || |||||||||||||||||||||||||||||||||   |||   ||    |  ||||    | |   |  ||  || |    ||  |||     |||||| |  |   |||| |  ||    |   ||||  | |                                             
TAAGAAGGGCAAGGATAGCATGTCTGCCCAGGGAAAGCGTCGTTATGACCGCAAGCAGTCAGGACATGGTGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtaa--tgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G160351_T03 (Zea mays), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggcagttcactctcagaattttaggatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt---
                                | ||| |  | |||||| | ||||| || ||||| || |||||||| |||||||| ||||||||||||||      |  | ||   ||    || || |          |||    |    ||  |  ||    | ||| | | |   | | |   | || ||| |     
CAAGAAAGGTAAGGATAGCCTTTCAGCTCAAGGGAAGCGACGTTATGACCGCAAACAGTCTGGATATGGTGGTCAGACAAAGCCTGTTTTCCACAAGAAGgttcaacacaaattctctactgtttgcagtaccaattacatactgaaggctgcttttggagttc--ttaatgcggatcctttatttact-tgcttcctaacat

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G160351_T01 (Zea mays), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggc----------agttcactctcagaatt-ttaggatgtctcgtcaat---cctgctatctcagtgtttgtgtttcgtgt-------
                                | ||| |  | |||||| | ||||| || ||||| || |||||||| |||||||| ||||||||||||||      |  | ||   ||    || || |               ||    || |  || || |||    |  || |  ||   | |||| ||  |   ||     ||||          
CAAGAAAGGTAAGGATAGCCTTTCAGCTCAAGGGAAGCGACGTTATGACCGCAAACAGTCTGGATATGGTGGTCAGACAAAGCCTGTTTTCCACAAGAAGgttcaacacaaattctctactgtttgcagtaccaattacatactgaaggctgcttttggagttcttaatgcggatcctttatttacttgct-tcctaacattaactcttcggtctattcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatg-ttgcgtaatcagcacctgatgaagcatgggcag-ttcactctcagaat---tttaggatgtctcg-tcaatcctgctatctcagtgtt-tgtgtttcgtgt------------------------------------------
                                | ||| |  | |||||  | |||||||| || || ||||||||||||||||| |||||||||||||||||||  | || |   |    | ||||     ||       |||  | | ||||    |||||||| ||    |  |  |||  |  |  || || |  |  |  | |                                          
TAAGAAAGGTAAAGATAGCCTTGCTGCCCAAGGAAAGCGTCGTTATGATCGTAAACAATCTGGTTATGGAGGTCAGACCAAGCCCGTCTTCCACAAGAAGgtatactcgcttttccttgtcttgatctctaattactgtcttctatgtgagaaccaatttaggatttcagaattgactctgtgaaatatgtcttataggaatgatttgttaattggaccttgctcattatttgtctttctttggaacag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT3G23390.1 (Arabidopsis thaliana), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatga-------agcatgggc--agttcactctcagaattttaggatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt---------------------------------------------------------------------
                                | ||| |  | |||||| | |||||||| || || || |||||||| ||||||||||||||||| ||||||   |   | ||||     ||||         ||  ||      ||  | |      |  | |||  || |     | ||   |||   ||  |||  |    | |                                                                      
CAAGAAGGGTAAAGACAGTCTTGCTGCTCAAGGAAAGCGTCGTTATGACCGTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv01s0011g02080.t01 (Vitis vinifera), 5'ss of exon 3
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgta-tgttgcgt---aatcagcacctgatgaagcatgggcagttcactctcagaattttaggatg--tctcgtcaatcctgctatctcagtgtttgtgtttcgtgt------------------------------------------
                                | ||  |  | |||||  ||||||| ||||| || ||||| |||||||| |||||||||||||| ||||||    | | |    |||   |  |  |     ||    |   |  | |   | || |  |||   | ||    |   |||||| |   | ||| | |  |   |                                          
CAAGAAAGGAAAAGATAGCCTTGCAGCCCAGGGGAAACGCCGGTATGATCGGAAACAGTCAGGCTATGGAGGACAGACCAAACCTGTCTTCCACAAAAAGgtaacaatccatctatatccttatttccttggaaattt-taaccctttttttaagttgtgtgatacttttctcagagattgctatttatatttttatatgccaaattttcataacctttgattgcttttcacctaatcacctaatcag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 5'ss of exon 2
--------------------------------GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgta-----------tgttgcgtaatcagcacctgatgaagcatgggcagtt-cactctcagaattttaggatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt-------------------------------------------
                                | ||| | || || ||| | ||||||||||| || ||||| ||||| || || ||||||||||||||||||           | | || |  ||  |  |     ||  ||     ||| ||   |    ||  |  ||   || ||      |   |  || ||  | |    |  |                                             
CAAGAAGGGTAAAGATAGCTTAGCTGCCCAAGGAAAGCGCAGGTACGACCGCAAACAATCAGGTTATGGAGGACAGACAAAACCCGTCTTCCACAAGAAGgtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccag

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EDP05070 (Chlamydomonas reinhardtii), 5'ss of exon 3
GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggcagttcactctcagaattttaggatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt-
| ||| |  | || ||| | || || || || ||||| |||||||||||||| |||||||||||||||||  |   |  |    || |   |||      | | |  |     |    |   | |   |    |       ||    || |||| | | |   ||  | 
GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAGgtgcgcgacagagctggcgcggcatgttatgggcgtatcttgaagtggtgaccgtggaggggtgggggtggggtgagg-ctgagtgctggcgcagcggatg

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|18368682|gb|BJ200767.1|BJ200767
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162262338|gb|FC437665.1|FC437665
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162228552|gb|FC404150.1|FC404150
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|18335674|gb|BJ167694.1|BJ167694
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|18360736|gb|BJ192799.1|BJ192799
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162225415|gb|FC401193.1|FC401193
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|162221524|gb|FC397541.1|FC397541
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|67575316|gb|BJ948140.1|BJ948140
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|67698779|gb|BJ959012.1|BJ959012
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
EST: gi|18327408|gb|BJ159410.1|BJ159410
EST:     GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG
genomic: GGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAG

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), 31 (downstream exon)
Score: 39

GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcg ... tttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtatgttgcgtaatcagcacctgatgaagcatgggcagttcactctcagaattttaggatgtctcgtcaatcctgctatctcagtgtttgtgtttcgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG