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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG

Basic information

species Physcomitrella patens
transcript PP1S225_37V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 5
aaagtatcattctctatcgttttattttattttattttatttatttatttca-tctatctgtttgaggagcactg--tcttagtgataagtt--cgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
                |  ||| ||   |||   ||  | |||| |||||   | | |   | | | || || ||  ||||  | |    |   ||| | |||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||||  |||  ||||  | ||||| ||||| || ||||| ||  ||
---------------gtaatttcatg--attcctttgaaattatctattttgctttgtacttgtaatgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 5
aaagtatcattctctatcgttttattttattttattttatttatttatttca-tctatctgtttgaggagcactg--tcttagtgataagt--tcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG--------
                |  ||| ||   |||   ||  | |||| |||||   | | |   | | | || || ||  ||||  | |    |   ||| | |||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||||  |||  ||||  | ||||| ||||| || ||||| ||  ||        
---------------gtaatttcatg--attcctttgaaattatctattttgctttgtacttgtaatgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGGTTTGACT

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
aaagtatcattctctatcgttttattttattttattttatttatttatttca-tctat-ctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
   |||    |  || |  || ||| | ||   |    | |   |||| | | | | | |  ||   |  ||     ||   ||||   |   | | || ||| || ||||| || ||||| ||||||||||| ||||| ||||||||||||   ||  ||||  | |||||||| || || || |||||  ||
---gtagtgattcctctgattctatct-ataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
  | | ||||  | || | | |  |    |||  ||||||||||||| ||| |  |    | | | |   |      |  ||||||  |    ||| |||| |||||| | || || || ||||||||||| ||||| |||||||||||| | || |||||  | ||||||||||| || ||||||||||||
gtaatgtcatcat-taacatatagtcagctttagttttatttatttaattc-taaaaagatataatgtttatc--tctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 5
--aaagt-atcattctctatcgttttat--tttatttta-ttttatttatttatttcatcta-tctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
  || || |||| ||   ||     |||  |    |||| ||||||||| ||| ||||   | | | | |     ||       || ||||||  |||  ||| |||| |||||| | || || || ||||||||||| ||||| || ||||||||| | || |||||  | ||||||||||| || ||||||||||||
gtaatgtcatcactcatcattaacatatagtcagctttagttttatttacttaattcaaaaaatatatatataatgcttatcactattgataacatcgcatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 5
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatct-gtttgaggagcactgtcttagtgataagttcgat-tatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
   |||   || |||     ||   ||| | |||||| ||||||| ||   ||  |||| |||||     |||| |   |    |||   | || | | |||| |||||| | || ||||| ||||||||||| || || |||||||||||| | || |||||  | ||||||||||| || |||||||| |||
---gtaaggttatcttctagttagctttttgttatttgatttatt-ataagattcatcttgtttgt----cactatggaaaatctaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 6
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
   |||   |  |||     ||  |||| | |||||| ||||||  |||     | | ||| |     | | | | | |    || |||      | |||| |||||| | || ||||| ||||||||||| || || |||||||||||| | || |||||  | ||||||||||| || |||||||| |||
---gtaaggtcatcttatagttagtttt-tgttatttgatttatagattcttgttgtttgtctctatggaaat-tttaaacactatgtt------tacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G10740.1 (Arabidopsis thaliana), 3'ss of exon 6
-aaagtatcattct-ctatcgttttat-tttattttattttatttatttatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
  ||||| ||     |||| |   ||| ||| |  |  || ||    || ||||| |     ||   |     |  |   |  | ||   |   | ||   ||| |||||| | ||||| || |||||||| || ||||| || |||||||||||||| |||||  ||||||||||||| || |||||||| |||
gtaagtagcaagaaactataggactatatttctgctgcttcat--gcttttttcaacatatagtcctaattataggggtgtgttcattcata-aactaaatagGAACTTGGAGGGTAGGAGGAGTTCTTGCAGTTTCTCGTGCGTTTGGTGATCGGCTTCTGAAGCAATATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 5
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtctta-gtgataagttc---gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
                          | |    |     |  | |||||||      |  |||| ||   | | ||    |||   |  ||   ||||   |||| |||||| | || || || |||||||| || || || || |||||||||||  |||| ||| ||||||||||||| || ||||||||||||
-------------------------gtaacaagaaaccgtagagttatttc-----ccgctttgtggcttattttccggtgtgcctaactcctagattgaacagGGACTTGGAGAGTTGGAGGAGTTCTTGCAGTTTCCCGCGCGTTTGGTGATCGATTGCTTAAACAATATGTTGTTGCTGATCCAGAAATTCAG

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|208395549|gb|DC928964.1|DC928964
EST:     TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTG                         GTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
genomic: TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTGgtgagcatct ... gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
EST: gi|162279026|gb|FC454765.1|FC454765
EST:     TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTG                         GTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
genomic: TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTGgtgagcatct ... gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
EST: gi|100407639|gb|BY991783.1|BY991783
EST:     GATGAACGACAACGCATTGAAAAGGCTGGGAG-AGTAGTCATGTGGTCTG                         GTACTTGGCGTGTANGTGGCGTTCTTGCTGT
genomic: GATGAACGACAACGCATTGAAAAGGCTGG-AGGAGTAGTCATGTGGTCTGgtgagcatct ... gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGT
EST: gi|162249046|gb|FC421493.1|FC421493
EST:     TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTG                         GTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
genomic: TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTGgtgagcatct ... gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
EST: gi|208351977|gb|DC925786.1|DC925786
EST:     TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTG                         GTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC
genomic: TGATGAACGACAACGCATTGAAAAGGCTGGAGGAGTAGTCATGTGGTCTGgtgagcatct ... gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG
                                     ataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT