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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA

Basic information

species Physcomitrella patens
transcript PP1S77_89V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 11
-----------------tgaaaacctcctgtctatgttgct-------agtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacga--tatttgtctgttcgttgtgt-----agATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA
                 |   || ||| | | | || | ||        ||  | ||     ||     |  ||  | |    || || |      || | |  ||||  |    || |  | |     |||||||||||||||| ||||| || || || || ||||| ||||||||||||||  ||||    ||||| ||  | ||| |  || |||| ||||| ||  
gtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaacacatt-gtttacatattgctctgtctaattattcctactctcataatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 10
tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA
 | ||||   | |      | | ||    | ||  | |||||  |  || | ||||   ||   |    |  | ||  |||   |    |  |  |  ||||||| || |||||||| ||||| |||||||||||  ||||||| ||||| ||||| ||   |||||| ||  ||||| |  |||||||||  || ||  
-gtaaactgtcagc-----tggataacttttttagtttttaattcagaagtacttcttatt-tgatatcttgttactttatccctaatatgctatttcagATGGCAGAATATAGGATTTCAATCTACGGAAGGAAACAGAGTGAATGGGACCAACTTGCAAGTTGGATAGTGAACAATGAATTGCACAGTGGAAATGTTG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 10
-----------------------------------tgaaaa----cctcctg----tctatgttgctagtactctttatctttaaaactaa--aatccttccacttgcaaagaatca--tgacgatatttgtctgttcgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA
                                   || ||      || |||      ||| || ||||||  || | |  |  |  |||   | || ||   || | || ||  ||  | | |||  |||    | | ||    |||||||||||||| ||||||| ||||| || |||||||| || || ||||| ||| ||||   |||||| ||  ||||| |  |  | || ||||| ||  
gtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgt--gtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA
     || |  || | ||  |  ||  | |  ||  || ||      | || ||    |      |||         || | |||   ||  || |    |||||||||| ||||| |||||||| || || |||||| | ||||||||||| ||||| |||  |||||| ||  | ||| |  || |||| ||||| ||| 
-ttggacttgttgacaataat-ttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 10
tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgt--gtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA
     || |  || ||||  |  ||  | |  ||  || |       | || |||   |      |||         || | |||   ||  || |    |||||||||| ||||| |||||||| || || |||||| | ||||||||||| ||||| |||  |||||| ||  | ||| |  || |||||||||| ||  
-tttgacttgttgactataat-ttaccatttcttgactgttgtttatatatgcttatccccatctagatgttaacttatttctgtgacttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTG

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|162268981|gb|FC445473.1|FC445473
EST:     CAGAGTTGACTAAGGAAGTTTTCTCAGATCTTCAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGAT
genomic: CAGAGTTGACTAAGGAAGTTTTCTCAGATCTTCAAGCAAGTAAATATCAGgtgtgtgaac ... cgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGAT
EST: gi|162171488|gb|FC346763.1|FC346763
EST:     CAGAGTTGACTAAGGAAGTTTTCTCAGATCTTCAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGAT
genomic: CAGAGTTGACTAAGGAAGTTTTCTCAGATCTTCAAGCAAGTAAATATCAGgtgtgtgaac ... cgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA
 aactaaa  putative branch site (score: 2)
                                       tctgttc  putative PPT
                                atatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgtgtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC