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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA

Basic information

species Physcomitrella patens
transcript PP1S188_35V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g51200.1 (Oryza sativa), 3'ss of exon 1
-----------ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
             | ||||   ||  | ||      |   ||  || |     |||      |      |||||  ||   |    || |  ||       |||  || |||| || |||||||| || || || ||||| ||||||||||||||  | ||||| || || ||||||||||| |||||||| ||||| |||||||| || |
gtaaaccccatcccttcccctcccgctcgatccgcgtgggatcttccgatctcgtgtcccccga-----atcgtgtgttctgatcaccca--ttggctgtgttaatcgcagGTGCTGGAGCTGGCCGGGAACGCGGCGAGGGACAACAAGAAGAACAGGATCGTGCCGCGGCACATCCAGCTGGCGGTGCGCAACGACGAGGAGCTGAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g34510.1 (Oryza sativa), 3'ss of exon 1
ttcgtc-cctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
   ||  |||| |||  |      |    |    ||      |  ||  |  | ||  |    |  ||    | |         |     |||  ||| |||| || |||||||| || || || ||||| |||||||||||||| || ||||| ||  | ||||||||||| |||||||| ||||| |||||||| || |
---gtaacctcaccatctccctcttccgcccccttcgccgccgccgcgcgccgcttggggatttgggtttaatctcatggggggtttgtgattgggcgcagGTGCTGGAGCTGGCGGGGAACGCGGCGAGGGACAACAAGAAGAACCGGATCGTGCCGAGGCACATCCAGCTGGCGGTGCGCAACGACGAGGAGCTGAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G046055_T01 (Zea mays), 3'ss of exon 1
-------ttcgtccctctccaattgaagtatattt-cattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
         || |||       |      || ||  |    ||||     || | |  | |||   ||||    |   |||   | |   ||       | | || |||| || |||||||| || || |||||  | |||||||||||||| |||||||| || |||||||||||||| |||||||| ||||| |||||||| || |
gtaatcccccgacccctcttcctctcttcatgttcaccagatctgctcttgtccgatctcgtttgaatcgccgtt---gtgaatcgattgtttccttcgtttccgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGTATCGTGCCGCGCCACATCCAGCTGGCGGTGCGGAACGACGAGGAGCTGAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G107540_T01 (Zea mays), 3'ss of exon 1
-------------ttcgtccctctccaattgaagtatatttcatt--ctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
                 | | ||  |  |||  || ||     |   | | ||   |||     |  |||   |||    ||  |||| | | |   ||       | | || |||| || |||||||| || || |||||  | |||||||||||||| || ||||| || |||||||| ||||| |||||||| ||||| |||||||| || |
gtaatcccccgccccacttcttcctctcttgctgtttaccaggtctacgccggtccggtctcgat--gtttgaatcccccgt--cgtgagtcgattgtttccttggttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATCGTGCCGCGCCACATTCAGCTGGCGGTGCGGAACGACGAGGAGCTGAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM5G883764_T02 (Zea mays), 3'ss of exon 1
--------ttcgtccctctccaattgaagtatatttcattctctggaagggt---gcaagttggttaagatcgttagt-aacgtgtgcctaac-tttagaacattatgc--gtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
         || ||    |     ||   |  |||||  ||||        |   || | |  |||  |||  ||  | ||  | |||   ||  | | ||   | |||  | ||||  | || ||||| || || || ||| | |||||||||||||| || ||||| || || ||||||||||| || ||||| ||||| ||||| || || |
gtaactgcctcctcttcttttccctgccctccatttctctctccccctccctttagcgaatccgtttggatgtttgttgaatctttgcggtacgctcataatcgtttgcctgcagGTGTTGGAACTGGCGGGCAACGCGGCGCGCGACAACAAGAAGAACCGCATCGTGCCGCGTCACATCCAGCTCGCCGTGCGCAACGACGAGGAACTCAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G42760.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgc-ctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
                                                                              ||  |   |      ||  | | | | |  |  ||||   |     |  ||  ||   |||  | | |    ||    | |   |      || ||  |||||| | ||  ||||||| |||||||| || || ||||||||||||||||| || ||| | ||||| ||||| || ||| | |||||||||||||| || |
gtttgttttggattgtcgattaggtttagatttgattagttcttgtgtttttgatcagtctgtttggtcttggtttaatttttgttttaaagttttgattttttattgtgttctgattgacctaattttattttgaatcaatcgaatttggtttgttgatgatgtgtgtttttgtttagGTTTTGGAATTGGCTGGGAATGCTGCTAGGGATAACAAGAAGAATCGTATTGTTCCTAGGCACATTCAGCTTGCTGTGAGGAACGATGAGGAGCTGAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G54690.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------ttcgtccctctccaattgaagtatatttcattctctg--gaa-----gggtgcaagttg--gttaagatcgttagtaacgtgtgcctaactttagaacatt------atgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
                                                         ||||   |     ||      || ||||  | | |   |||     |  |   | |||  |||||| |   |  ||  || ||      | ||  |  ||      ||   |||||  | ||||| ||||||||||| || ||||| ||||||||||  |||||||| || || ||||| ||||| || ||| | |||||||| ||||| ||||
gtaacaaacaatcttctgtttggtatttagtcttttagtctctatgatgagaatcactcgtaattgatatatcactagatttttcgatgtttaccgaatctttgattttgatttgatgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv14s0030g00450.t01 (Vitis vinifera), 3'ss of exon 1
-ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgt-agGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
 || | |    |  ||   ||| |    |     | |    |  |     || | |    |   |    ||       |   || |     |  || || ||||| | ||||| ||||||||||| ||||| |||||||| |||||||| || || ||||||||||| |||||||| ||  | || || ||||||||||| |
ttttgacgaattggaacccaagaaagcataggattatacgggttttaggattcgctcttttgaatcaagactcaga--tggtttgatggtgtgttgagtcagGTTTTGGAGCTTGCTGGAAATGCAGCGAGGGACAACAAAAAGAATCGCATTGTACCTCGCCACATACAGCTAGCAGTAAGGAATGACGAGGAGCTAAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0104g00970.t01 (Vitis vinifera), 3'ss of exon 1
ttcgtccctctccaattgaagta--tatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaac-tttagaacat-tatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
       || ||||||   | |   |   | |    ||| |    || |  ||| ||    | | ||  | ||||   || |  | | |    | ||| |  ||||||| ||||| ||||| ||||||||||| ||||||||||||| | | ||||| || || ||||| ||||| || ||| | || ||||||||| | || |
--taattctttccaatgccactgcttgcctgagaaactgcactt-tgtagtttgtttgtttttgataa-atcgtggatctgatgtctgggttgtgtattcacagGTTCTCGAGCTTGCTGGCAATGCTGCGAGGGACAACAAGAAGAGTAGAATCGTTCCCCGGCACATTCAGCTTGCTGTGAGGAATGATGAGGAGTTGAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0104g00960.t01 (Vitis vinifera), 3'ss of exon 1
ttcgtccctctccaattgaa--gtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
             | |||||   |   |||  ||||||        |  | ||  |   ||       ||   ||   ||   |      | ||    ||||||| | ||||| ||||||||||| || || ||||||||||||||||| ||  ||||  | ||||| || || || ||| | |||||||||||| |  | |
-----------gtacttgaatctttccttttcttctctccgtttccgtcattttctctggacaaactttattttgacactgttt-----gcgtttcttgtagGTTTTGGAGCTTGCTGGAAATGCGGCCAGGGACAACAAGAAGAATCGGATTATCCCGAGGCACATACAACTTGCAGTGAGGAACGATGAGGAGTTGGGGA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ17602 (Selaginella moellendorffii), 3'ss of exon 1
ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
                    ||    ||| ||  ||       |    || |  | |     | | |  || |      | ||     ||||   |  ||||  | ||||| |||||||| || ||| | || |||||||||||||| ||| ||||  | ||||||||||| || ||| | ||||| |||||||| || |
--------------------gtgagattc-tttgctcatctcttttccgtcgtctcaatctctcaatctcggg------atttcgtcccatt---cccagGTGATCGAGCTCGCTGGAAACGCCGCGCGGGATAACAAGAAGAATCGGATCATCCCCAGGCACATCCAGCTCGCCGTGAGGAACGACGAGGAGCTCAGCA

upper sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ29068 (Selaginella moellendorffii), 3'ss of exon 1
ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
                    ||    ||| ||  || |     |    || |  | |     | |||  |  | |  |   ||     ||||   |  ||||  | ||||| |||||||| || ||| | || |||||||||||||| ||| ||||  | ||||||||||| || ||| | ||||| |||||||| || |
--------------------gtgagattc-tttgctcgtctctttttcgtcgtctcaatctctcagt--ctcgggatttcgttcgtcccatt---cccagGTGATCGAGCTCGCTGGAAACGCCGCGCGGGATAACAAGAAGAATCGGATCATCCCCAGGCACATCCAGCTCGCCGTGAGGAACGACGAGGAGCTCAGCA

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|2950257|gb|Z98084.1|Z98084
EST:     CTTGCTGCAGTGCTTGAATATCTANCTGCTGAG                         GTTCTTGAGCTGGCTGGAAATGCTGCGANAGACAACAAGAAGAATCGTATC
genomic: CTTGCTGCAGTGCTTGAATATCTAGCTGCTGAGgtgagcattt ... ttatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
                                taacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgtccctctccaattgaagtatatttcattctctggaagggtgcaagttggttaagatcgttagtaacgtgtgcctaactttagaacattatgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT