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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggttcggttctacttgcgttcagcaggttactaggtattatattattctttccgatctttttcttgctaggtttttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG

Basic information

species Physcomitrella patens
transcript PP1S138_84V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S138_84V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g01430.2 (Oryza sativa), 3'ss of exon 4
gtaagggttcggttctacttgcgt--tcagcaggttactaggtattatattattctttccgatctttttcttgctaggtttttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG
               ||  || |   || |||    || | || |   || | | ||  |  ||| ||  |    |         ||| | | |   |  |  | ||||   || | |           || |||||||| ||| | ||||| ||  |||| || ||| ||||||| |||||||| ||||| ||||||||||||||||| |||||||| ||||  |
---------------tagctgtggtgtctgcaatgcacaatgtctggaataactattcactctctcttcttcataaa--------acatggtttacta-aatttagaacctgatgata-----------tgtcagGTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAG

upper sequence: PP1S138_84V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 5
gtaagggttcggttctacttgcgttcagcaggttactaggtattatattattctttccgatctttttcttgctaggtttttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG
                      | |  |  |  | | | | |  ||||  |        |   ||  ||| ||    || | || || | |||      |||  |  || |  |   |  |     ||| |||||||| ||| | ||||| ||  | || || ||| ||||||| |||||||| ||||| |||||||||||| |||| |||||||| ||||  |
----------------------gctgtggtgtctgcaatgcacaatat-gtctggaataactattcactttct---cttcttcataaaacatggttt--actaaatttagaacatgatgat-----atgtcagGTGGAGCTTAAGGAAGGCCCCTTGGAACAGTTTACACATGAAATGGAACCCTTTCTACGCAAGCAAGGACTGCCAGTTCGTCTGAACAAAG

upper sequence: PP1S138_84V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv12s0034g01000.t01 (Vitis vinifera), 3'ss of exon 5
gtaagggttcggttctacttgcgttcagcaggttactaggtattatattattctttccgatctttttcttgctaggtttttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG
                             |    ||       | |  |  ||||| |    | || | |    | ||  |     | ||||   |  ||  |    |  |||  |    | |    |  |||||||| ||| ||||||| ||||| || || ||  ||||||| |||||||| || || ||||||||||| ||||| |||||  | ||||  |
----------------------------taaaacacagaaatctgtgatcatcttttca---tattgcatatatgattcatctc--atatatcctaacaaaatttcttgcattgaatccttaatatgtttcagGTGGAGCTTAAAGAAGGTCCTCTTGATCAGTTCACACATGAGATGGAACCCTTCCTACGCAAGCAAGGGATGCCGGTTCGGTTGAACAAAG

upper sequence: PP1S138_84V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ38547 (Selaginella moellendorffii), 3'ss of exon 4
gtaagggttcggttctacttgcgttcagcaggttactaggtattatattattctttccgatctttttcttgctaggtttttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG
                                                  | | |   ||   |  | ||||     ||||||      |   ||  | |      || | |   |||    ||     ||||||||||||  | ||||| || || ||||||||  | || || ||||| |||||||| || ||||||||||||||||||||||| ||||| |
-------------------------------------------------gtgcgtgtagacaatgcttttgc-----ttttgcgtggttttcttcgtgta-----gctcactgtgagtgactac-----acagGTGGAACTCAACGAAGGCCCACTGGAGCAATTCACGCACGAGATGGAGCCATTTCTGCGAAAGCAAGGAATGCCTGTTCGTCTAAACAGAG

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|162190026|gb|FC366600.1|FC366600
EST:     AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
EST: gi|37834545|gb|BJ592557.1|BJ592557
EST:     AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCCAATTTTCACATGATATGGAACC
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAG-CAATTTTCACATGATATGGAACC
EST: gi|37825557|gb|BJ583623.1|BJ583623
EST:     AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCCAATTTTCACATGATATGGAACC
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAG-CAATTTTCACATGATATGGAACC
EST: gi|162190025|gb|FC366599.1|FC366599
EST:     AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
EST: gi|67696545|gb|BJ956778.1|BJ956778
EST:     AGTTTGAAGAGCTTGATTTNGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
EST: gi|37822604|gb|BJ580670.1|BJ580670
EST:     AG-TTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
EST: gi|67694612|gb|BJ954845.1|BJ954845
EST:     AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACG                         GTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA
genomic: AGTTTGAAGAGCTTGATTTTGCACGGACTGGTAGCGTTGCGACTGAGACGgtaagggttc ... ctgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG
                          aactaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggttcggttctacttgcgttcagcaggttactaggtattatattattctttccgatctttttcttgctaggtttttgcacaagatatgtcacgaacttgaactaaattacagttgtcactgatgacagGTGGAACTTCAAGAAGGACCTCTAGAGCAATTTTCACATGATATGGAACCATTTCTTCGCAAGCAAGGAATGCCTGTTCGTCTTAACAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA