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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgaaatggagctccactgccgaggacgtccattgctaagcccaaatctgatttagaaacgaacagatgcctgatccgaatcatggttctgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT

Basic information

species Physcomitrella patens
transcript PP1S1_629V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_629V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g39610.1 (Oryza sativa), 3'ss of exon 1
gctgaaatggagctccactgccgaggacgtccattgctaagcccaaatctgatttagaaacgaacagatgcctgatccgaatcatggttctgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT
         |  |    |   |  | | ||  ||    || |  || |    | || |     || |          |  |  |   |    || |||||||| ||| ||||||| ||||||| ||||||||| || || |   |||| || |||||||||| ||| |||||| | |||||||||||||||||||| || 
---------gtacgtagcgtacatgcatgtatata--caaacataagtactgtatatatgtacactgcaattgctaacatacaagtatatatatgtgcagGTATGGACCTGACCGTCCCAAGTACCTGGGCCCGTTCTCGGAGCAGACGCCATCGTACCTGACCGGAGAGTTCCCGGGAGACTACGGGTGGGACACGGCG

upper sequence: PP1S1_629V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G414192_T01 (Zea mays), 3'ss of exon 1
gctgaaatggagctccactg-ccgaggacgtccattgctaagcccaaatctgatttagaaacgaacagatgcctgatccgaatcatggttctgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT
   | |   |   ||  ||  |||    | ||| |||       ||  || | |   |||  ||  |     ||||   |  |  ||| |      |||||||||||  |||| || |||||||  || ||||| || ||||   |||| ||||||||||||| |||||||||| | || |||||||||||||||||||| 
---gtacgtgccttctgctctccgcatgcttcccttgtgtcaatcagctc-gctcgggaagtgagaa-----ctgacgtgcgtgctggctgcctgctgcagGTACGGCCCTGATCGCCCCAAGTATCTTGGCCCGTTCTCCGAGCAGACGCCGTCGTACCTGACCGGCGAGTTCCCCGGCGACTACGGGTGGGACACCGCG

upper sequence: PP1S1_629V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G105518_T01 (Zea mays), 3'ss of exon 1
gctgaaatggagctccactgccgaggacgtccat--tgctaagcccaaatctga-----tttagaaacgaacagatgcctgatccgaatcatggttctgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT
      | |     ||   ||||    | | | |    |||||   | |  |||      | || |||  |||||  | |   | || |  || | |     ||||||||||   ||||||| ||||||| ||| | ||| || ||||   ||||  ||||||||||||  ||||||||| | || |||||||||||||||||||| 
----gtacgtgctccctgcgccgcattcattcgtgtcactaagaggagaggtgaggactgtgagtaactgacagacacgtacgctgactgctgctgca----tgcagGTACGACCCTGACCGCCCCAAGTACCTTGCCCCGTTCTCCGAGCAGACGTCGTCGTACCTGACGGGCGAGTTCCCCGGCGACTACGGGTGGGACACCGCG

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|162262452|gb|FC439495.1|FC439495
EST:     GCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|67698714|gb|BJ958947.1|BJ958947
EST:     GCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|18338024|gb|BJ170048.1|BJ170048
EST:     AGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: AGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162260163|gb|FC436298.1|FC436298
EST:     GTCACCATGCGTCGAACCGTCAACAAGTCGGCTGGCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162204589|gb|FC381973.1|FC381973
EST:     GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTG                         GTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|208378189|gb|DC918810.1|DC918810
EST:     GCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|208348686|gb|DC926361.1|DC926361
EST:     GCAGCGACAGCATNT-                         GTA-TGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162276486|gb|FC452164.1|FC452164
EST:     GCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162214182|gb|FC390228.1|FC390228
EST:     GTCACCATGCGTCGAACCGTCAACAAGTCGGCTGGCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|208354288|gb|DC957466.1|DC957466
EST:     GTCACCATGCGTCGAACCGTCAACAAGTCGGCTGGCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162203664|gb|FC379150.1|FC379150
EST:     GTCACCATGCGTCGAACCGTCAACAAGTCGGCTGGCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162215789|gb|FC390854.1|FC390854
EST:     CAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTCCCGGCGAGACCCC
genomic: CAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|162153728|gb|FC329131.1|FC329131
EST:     GTCACCATGCGTCGAACCGTCAACAAGTCGGCTGGCAGCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
EST: gi|67698321|gb|BJ958554.1|BJ958554
EST:     GCGACAGCATCTG                         GTATGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC
genomic: GCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 25 (upstream exon), 16 (downstream exon)
Score: 6

TCAAGCCCGTCAATGAGCTGTCCCGCAGGGTGGGCAATGTCGACGCCCGCGTCACGATGCGTCGGACCGTCAGCAAGTCCGCTCGCAGCGACAGCATCTGgtattacccc ... tgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctgatttagaaacgaacagatgcctgatccgaatcatggttctgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT
                                          ttctgat  putative branch site (score: 6)
      atttagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgaaatggagctccactgccgaggacgtccattgctaagcccaaatctgatttagaaacgaacagatgcctgatccgaatcatggttctgatttgcagGTACGGAGCTGACCGACCCAAGTTCCTGGGCCCCTTTTCCGGCGAGACCCCGTCGTACCTGAACGGCGAGTTCGCTGGAGACTACGGGTGGGACACCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagatgc