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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatcgtctctcttccgaggtctatcgtttgagagacctatcatgtaacggataaacttctgagacttactatggaacgctcctggaacatcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC

Basic information

species Physcomitrella patens
transcript PP1S38_353V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os10g35850.1 (Oryza sativa), 3'ss of exon 2
agaatcgtctctcttccgaggtctatcgtttgagagacctatcat-gtaacggataa-acttctgagactta--ctatggaacgctcctggaacatcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
    | ||     | |  || || | | ||    |    | || | |   |  ||     ||     || ||  ||  | |||            ||    |||    || ||||||||||| |||||||| ||| | |||||||| ||||| ||||| |||||  |||| || ||||| ||||||    | ||||||||||  
----ttgttatcttcctcagttcaaactttcagtaatattgtctttgcctcatattgtgtttactgcacataaccttcgtaactaaatgattttctctgtgcagATTGTTCTATGGACCTGGTGGACCATATGCATTGTTTGCTGGTAAAGATGCCAGTAGGGCGTTGGCGAAGATGTCCTTTGAGCCACAAGATCTGACTGAT

upper sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G107444_T01 (Zea mays), 3'ss of exon 1
-----agaatcgtctctcttccgaggtctatcgtttgagagacctatca-tgtaacggataaacttctgagacttactatggaacgctcctggaacatcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
      |||||   |||||  |   ||| |  |          || | | | | ||   |  | |||||  | |||  |||         | || |   ||  |||    || ||||||||||| ||||||||||| || || || || |||||||||||||| || || || || ||||| || |||    |||||||||| |||
agttgtgaatcaa-tctctctca--gtccacagccccgcccttcttttacttttacatgttgaattctgt-atttataatgtt-tatcaattgacccctgtg-cagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGCCAGCAGAGCCCTAGCGAAGATGTCCTTCGAGCCACAGGATCTGACCGGC

upper sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G25940.1 (Glycine max), 3'ss of exon 1
----agaatcgtctctcttccgaggtctatcgtttgagagacctatcatgtaacggataaacttctgagacttactatggaacgctcctggaacat--cgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
    | | |  | | ||||  ||  ||||   ||  |      | |||   |    |||   ||         | | |  || | | ||| ||  |  | || |||    |||||||||||||| ||||| || || || |||||||| || || || ||||| ||| | || |||||||||||||| ||||| ||||| ||||| 
tattatattgatttttcttttgatttctacttttaaa------tgtcaccaacaatatatgttttccttttccatttttcaatgtttctgtaatgtgccctaccagAATGTTTTATGGACCTGGTGGACCCTATGCTCTATTTGCTGGCAAGGATGCTAGCAGAGCTTTAGCAAAAATGTCTTTTGAAGAGAAAGATCTAACTGGA

upper sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G29660.1 (Glycine max), 3'ss of exon 1
agaatcgtctctcttccgaggtctatcgtttgagagacctatcatgtaacggataaacttctgagacttactatggaacgctcctggaacatcgtaa----cagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
 ||||    | | | | ||  |   | ||||        |||  | ||   ||||   | || | ||    |||      |   |||||    ||      ||||   |||||||||||||| ||||| || || || |||||||| || || || ||||| ||  | || || ||||||||||| ||||| ||||||||||| 
-gaatgaaatatgtgctgattttatttgtttcttta---tatgttttatttgatagggtgctaacaccccttatttttatcatgtggaattgtgtccttcccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCAAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG

upper sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
agaatcgtctctcttccgaggtctatcgtttgagagacctatcatgtaacggataa-acttctgagacttactatggaacgctcctggaac---atcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
   || ||     | |     ||| |  |||     || |||  | |||  ||||   ||       |||  |||      | | |||||     ||    ||||   |||||||||||||| ||||| || || || |||||||| || || || ||||| ||  | || || ||||||||||| ||||| ||||||||||| 
--tattgtgctgatgcttttttctttttttttcattacatat--tttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG

upper sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv16s0100g01280.t01 (Vitis vinifera), 3'ss of exon 1
agaatcgtctctcttccgagg---tctatcgtttgagagacctatcatgtaacggataaacttctgagacttactatggaacgctcctggaacatcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
   || |   |||     | |   | | |  |||       |||| |    ||    |||||||| |  ||| |  |  |  |   ||         |  ||||  ||| ||||||||||| || ||||| || || ||||||||||| || || ||||| ||||| || |||||||||||||| ||  | ||||| || || 
-ttattgctactccattaaaggcttttctattttctattttctattactccacactgaaacttctta--cttgcctttaattgaaactcatcatctcttgcagGATATTCTATGGACCTGGTGGTCCATATGCTCTGTTTGCTGGGAAGGATGCTAGCAGAGCTCTCGCTAAAATGTCTTTTGAAGAACAAGATCTAACAGGA

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|18348128|gb|BJ180175.1|BJ180175
EST:     CCTTTGTTGATGGCCATCAAAGCTCAGATTTATGATGTTTCTCGGTCAAG                         GGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGC
genomic: CCTTTGTTGATGGCCATCAAAGCTCAGATTTATGATGTTTCTCGGTCAAGgtatgtgagg ... atcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacggataaacttctgagacttactatggaacgctcctggaacatcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC
                   gacttac  putative branch site (score: 2)
       ataaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatcgtctctcttccgaggtctatcgtttgagagacctatcatgtaacggataaacttctgagacttactatggaacgctcctggaacatcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA