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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatgatagttgccccactacagcgcgtacttgtgaactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG

Basic information

species Physcomitrella patens
transcript PP1S1_203V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 3
acctgaatgt--tatagtgagg-ttctacaagcttgggctccccgatctgggctggttttatgatagttgccccactacagcgcgtacttgtgaactat-gcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
     |||||  | | || |   || | | |   |   || | | ||||  | |  | | ||  |   |||         |    | | | |   || | ||||| || || ||  | || || |||||||| || |||||||||||||||||||| |||||  ||||||||||      ||| || || |||||| |  || |
---aaaatgttttgtggtaatcctttttccattattaacttcac-atctatgatattctgattttccatgctatttgcttgttatttcctttattcttttgcagGTTTTCCTATACTTGGAATAGAATGGCAGAAAATGGAAAATCCTGATCTCCGAAAGGCAATGGGAATGAAATCTGACCAAAAGGGTGTTCGTGTCAGAAG

upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 3
acctgaatgttatagtga--ggttctacaagcttgggctccccgatctg--ggctggttttatgatagttgccccactacagcgcgtacttgtgaacta--tgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
      |   ||| || |    |||||      |||  |     || ||     ||||||| |||  ||| |   | |  |     | | |||    ||  | |||||||||| ||  | || || |||||||| || ||||| |||||||||||||| || ||| ||||||||||       || || || |||||| | ||| |
-----cagtctatggttaccacttctatctttctggtattttacatttgccacgtggttttttgaaggttccgttatt-taatatcttcatgtattataatttcagGATTCCCTATACTTGGAATAGAATGGCAGAAAATGGAGAATCCTGATCTCCGCAAAGCGATGGGAATGAAACCTGATCAAAAGGGTGTTCGTGTTCGAAG

upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatg-atagttgccccactacagcgcgtacttgtga------actatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
       | |||   |||  || ||| |   |    ||     |     || |||  |   || ||   |  | |   |   ||| || |        | | |||||| ||||| ||  | || || ||||||||||| |||||||||||||||||||| |||||  |||||||||| |  | ||| || || ||||| |||||| |
----ttttattaatttgaaattgtacta---tataatctgatgtgcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttcattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG

upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatgatagttgccccactacagcgcgtacttgtgaactatgc-agGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
              || || |||  | |   ||          | ||   |   | | | | |  |||     |    | | ||||||  |||| |   ||| || ||  || | || ||||| |||||||||||||||||||||||| | |||||| |  |||| ||| |       || || || || || ||  || |
--------------gtaagtttcaccga---tgattaatgttgtttgttatctatctct-acatgtgctttttt----ctcatacttg--aactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG

upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 3
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggtt--ttatgatagttgccc-cactacagcgcgtacttgtg-----aactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
        |  | |  |||     ||||  || |  |    |   |  ||   ||  ||   || | ||||  | ||  | | |||  | |       |||    |||||||||| ||| | ||  |||||||||| |||||||||||||||||||| ||   | |  |||| |||         ||||| || || |||||  || |
--------gcaaaatggagacaacacaaattttgtgtttttgtgttctgcatattgcttgaaattgctgcctacgcttaaactcgttttggcatttgtaacatcacagGATTCCCAATTCTTGGGGTTGAATGGCAGAAGATGGAAAATCCTGATCTGCGTGTGTCAATGGGGATGGGACCTGATCAGAAGGGTGTCCGTATTAGAAG

upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ30037 (Selaginella moellendorffii), 3'ss of exon 3
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatgatagttgccccactacagcgcgtacttgtgaactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
                |    ||| |  |    |||| |  | | ||      | | |     | |   | |  | |   | |         || || ||| || ||| | || |||||||||||||||| |||||||||||| ||||| ||||  ||| | ||||||||||  | ||| || || ||||||||||| ||
----------------gtatctctcctcgtcaaggcttct-gctttgctagcatataacttctgctttgctagcatataacttctgctctgcctctgaagGTTTTCCCGTGTTGGGTATTGAATGGCAAAGGATGGAAAATCCGGATCTTCGGAGAGCGGTCGGAATGAAGGCAAACCAAAAGGGTGTTCGTATACGCCG

upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ08981 (Selaginella moellendorffii), 3'ss of exon 3
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatgatagttgccccactacagcgcgtacttgtgaactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
                                    |  |    || | |  |  || || |  ||||     || | |   | ||      || || ||| || ||| | || |||||||||||||||| |||||||||||| ||||| ||||  ||| | ||||||||||  | ||| || || ||||||||||| ||
-----------------------------------gtatctctcctcgtcaaggcttctgct--ttgctagcatataacttctgctct--gcctctgaagGTTTTCCCGTGTTGGGTATTGAATGGCAAAGGATGGAAAATCCGGATCTTCGGAGAGCGGTCGGAATGAAGGCAAACCAAAAGGGTGTTCGTATACGCCG

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|162163954|gb|FC339864.1|FC339864
EST:     TGTTATTACTCACTTTATTACTGATTACGTCCGCAGCGGTGACTATACAG                         GATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCC
genomic: TGTTATTACTCACTTTATTACTGATTACGTCCGCAGCGGTGACTATACAGgtacgagtat ... aactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCC
EST: gi|162256228|gb|FC432284.1|FC432284
EST:     TGTTATTACTCACTTTATTACTGATTACGTCCGCAGCGGTGACTATACAG                         GATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCC
genomic: TGTTATTACTCACTTTATTACTGATTACGTCCGCAGCGGTGACTATACAGgtacgagtat ... aactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggctggttttatgatagttgccccactacagcgcgtacttgtgaactatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG
        ttttatgata  TA-rich tract