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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG

Basic information

species Physcomitrella patens
transcript PP1S87_157V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
        ||||  | |  ||    |        |      |  ||   | |  |  ||    |  || |  ||   |      || |   |  |  |||  | || |||| |||||||| || || || ||||| |||||||| ||||| |||||||| ||  | || |||||||| || |||||||||||||||||||| |||||||| || |
-------aagtgtacacatgtattctc----cttttattttttgcatgggcttctatgtttgtccaatatccgaagcacc---gatgaacataat-gtgtttcattattttgcagTATACACCAGCAATAGATATATGGAGTATTGGCTGCATATTTGCCGAGCTTTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
       |     ||||| |  |  | ||       |   |  | || | ||  ||| ||        ||   | ||   ||| |  |   |           | |||||| ||||| |||||||| || ||||| |||||  | || ||||||||||| ||| || | |  |||||||||||||| ||||| |||||||| || |||||  |||
------atgccatgctcttgaactatcgatacatatgcttagcataccaatt--tggataa-------tttcaaatgcacttgcaccatactaaactcaaatgtgttttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagt-tattgggtagaacatatttg---tgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
                                                        || | | || |  | | |  ||   |  | || |   ||  ||     ||  | ||   |   ||||  | |   |  ||||| |    | | |  | || ||||  |   |||| ||||| || ||||| || ||||| |||||| |||| ||||||||||| ||  || | || ||||||||||| || || ||||| |||||||| |||||  |||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagca-acagtgttttgagaatgttctcttagacattgtcgcattaggtgatatct--tgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtccctt-ttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
     | |  |||    |   |          | ||  ||||| | |    || |  ||  ||  ||| || |||     ||||| || | |     |||   || ||||||  ||||||| || ||||| ||||| |||||||| |||||||||||||| ||| |||| || ||||| || |||||||| ||||| ||||| || ||||| || |
----gattgttgcatatttccttctca-----cctgttccatggccctgtatagtttgtgaaa--tatctg-gagcaccattgaacaaatat----gtgttttttgttttttgtagTATACACCGGCGATAGATATATGGAGTATTGGCTGTATATTTGCAGAATTGTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 3
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
          ||| || | |||||   || |      ||  |   | || ||     ||| |   | || |    |   |  | |  | |||||  |  |    |||||||||||||||| || ||||| ||||| |||||||| || ||||||||||||||| | || || ||||| || |||||||| ||||| ||||| || ||||| || |
--------catgctcttttgttcataagaagcttc--actcttgtataa-ttgccttgtatagtttgttcg---atatctgaggaatactgttga-acattgtgtttttttacagTATACACCAGCGATAGATATATGGAGTATTGGTTGTATATTTGCGGAACTATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 3
-----gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgg-gtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
      ||    |    ||  | |      |    |   |  |     | |    || ||   ||  || |          | ||||||   || |       |  | |||  |||| ||||||||||||||||| |||||||||||  |||| ||||||||||| ||| || | |  || ||||| || || ||||| |||||||| || ||||| ||||
gtcggatagttttcacccggacacaacttctactagctcttcattgctatatggttttttactgtttaagagtacaccacttcattttgctgaatttacaacttaacacttaattttgcagTATACTCCTGCGATTGATATCTGGAGCCTAGGTTGTATATTTGCTGAAATGCTTATAGGGAAGCCTCTCTTTCCTGGCAAGAATGTGGTACATCAACTGG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
          | |     |  |  ||  |    |||||   |||   |  | |    ||   ||| ||||   ||     |   |    | |   | || |  |   |||| ||||| |||||||| || ||||| |||||  |||| ||||||||||| ||| || | || || |||||||| || || |||||||||||||| |||||| |||
----------tacttgaacagtgtgtacatagtgtggagtttgatgta--tcagcttgttttacaaattttatagaa---tcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G374088_T01 (Zea mays), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaa-gttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
            ||||  |  |  |      |  |  |   |    ||| ||| |||   | | | |  |  |   | || || |  ||    |  ||  |   || | | ||||||| || ||||| || ||||| ||||||||||| || || ||||| |||||  | ||||||| |||| | || ||||||| ||||||||| || ||  | |
-----------tcgctg-cactgggcactattaatttatttttttgcaaagttcttgttaacatcttcctattttatcatcttcaccaa-cactactaaat---ttgtatgtacagTACACCCCTGCAATTGATATTTGGAGTATAGGGTGCATTTTTGCTGAAGTTCTCACCGGAACGCCATTGTTTCCTGGGAGGAATGTTGTGCACCAATTAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
               |   |||       | |  |   |        |  ||| ||  |        | |    |   || | ||||  | | || ||   | ||| |||| |||||||| || || || || || ||||| || ||||| || ||||| ||| | ||||||||||| || ||||||||||||||||||||||||||||| || |
---------------tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggt-agaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
          ||  |  |  |||  ||    | ||| ||||| |    | |||||   | |   |  |  ||    || |    || |  | | || ||   | ||| |||| |||||||| || || || || || ||||| || ||||| || ||||| ||| | ||||| ||||| || ||||||||||||||||||||||| ||||| || |
----------tggacaatgtttctatgcttct-gtgtaccataatg--atttattatcttatcccggacctggacttggt---aaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaacac-tagtgcgct-ctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
|||| |   | | | ||  |   |   | |     || | |     ||||  ||||  |  |  ||| |  || |  | |    ||          ||||  |  | |||  | |||||||||||||| || ||||| ||||| ||||| || |||||||| ||| || | || || |||||| | || |||||||||||||| || || ||  |||
gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattat--gacaccaca-acctgaggttaaaacgga----------ttattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ38694 (Selaginella moellendorffii), 3'ss of exon 4
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttt-tttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
                                                 || |||| |      | |||   | || | |   | ||     |  | | | | || |  | | ||||| || || || || |||||||||||||| ||||||||||| || ||| | ||||| |||||||| ||||| ||||| ||||| || || || ||  | |
-------------------------------------------------gtgattgtg------acattgaagtgtaactccaagtagagtctaatgtttactttgtggtctgcagTACACGCCAGCAATTGATATCTGGAGTATTGGCTGTATATTCGCTGAAATCTTGACAGGAAAGCCGCTTTTTCCTGGAAAGAACGTAGTACACCAATTAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ31453 (Selaginella moellendorffii), 3'ss of exon 3
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttt-tttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
                                                      ||  ||  ||||  |   | || | |   | ||     |  | | | | || |  | | ||||| || || || || |||||||||||||| || |||||||| || ||| | ||||| |||||||| ||||| ||||| ||||| || || || ||  | |
-----------------------------------------------------gtgattatgacat--tgaagtgtaactgcaagtagagtctaatgtttactttgtggtctgcagTACACACCAGCAATTGATATCTGGAGTATTGGTTGTATATTCGCTGAAATCTTGACAGGAAAGCCGCTTTTTCCTGGAAAGAACGTAGTACACCAATTAG

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|162191647|gb|FC367692.1|FC367692
EST:     CCACAAGGTGGTATCGAGCTCCGGAGCTATGTGGTTCATTCTTTTCTAAG                         TATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTG
genomic: CCACAAGGTGGTATCGAGCTCCGGAGCTATGTGGTTCATTCTTTTCTAAGgtaacactag ... ttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTG
EST: gi|18366249|gb|BJ198327.1|BJ198327
EST:     CCACAAGGTGGTATCGAGCTCCGGAGCTATGTGGTTCATTCTTTTCTAAG                         TATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTG
genomic: CCACAAGGTGGTATCGAGCTCCGGAGCTATGTGGTTCATTCTTTTCTAAGgtaacactag ... ttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG
                                  ttatgtcccttttttt  CT-rich tract
                 attttgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG