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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttttctaacctttttgaatgtgtggaagtgcatttattttggtatgtgtatttcagtcgttcttttcagccatctaatgtgaacttactgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATATCATGGTTGCTTACAACAATAAGAAGTACTACATTGATATCATTGAATCG

Basic information

species Physcomitrella patens
transcript PP1S245_32V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------gacttttctaacctttttgaatgtgtggaagt-gcatt-tattttggtatgtgta-tttcagtcgttcttttcagccatctaat-----gtgaacttactggg--------tgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATATCATGGTTGCTTACAACAATAAGAAGTACTACATTGATATCATTGAATCG
                                          |   || || ||||          |  |  | | ||| |   | ||  |   |  | | ||| |   |||  | || || ||       ||| | |  | |         ||||| || || |  ||||||||||||||||||||||| || |  |||||||  || |||||||| || || || ||||||||||||||||||||  | ||  | 
gttagtaatttttcattaaatatttcttatcctagtgaaaacatccttttacccttccccttcccatatagtttgtattctgactagggttacatggtattagtagcgttttgaatccctcaaaacactaatgaccctgtttgtgttattcttgcagCTTGGAGAAAACTTTGCGGAACTTTTCTTGTCTAACTACAGGTGACAGCATTATGGTTGCATATAATAACAAGAAGTACTACATTGATATAGTAGAGACA

upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ38251 (Selaginella moellendorffii), 3'ss of exon 3
gacttttctaacctttttgaatgtgtggaagtgcatttattttggtatgtgtatttcagtcgttcttttcagccatctaatgtgaacttactgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATATCATGGTTGCTTACAACAATAAGAAGTACTACATTGATATCATTGAATCG
                     |  ||| | ||||    |   | |||  |    | |   |   || | ||   ||    | |   ||| ||   ||||| |||||||| ||  || |||| || || || || ||  | |||||||| |||||||| || |||||||| ||||||||||||||||||||  | ||| | 
--------------------gtaagtg-aggtgccaccagccttgtacttactctgctaacag-ctctccaa--attccgttttttcttgctt--tgcagATTAGAAACCACGCTGAGGAATTTCTCGTGCCTCACTGTGGGTGACAACATCATGGTGGCGTACAACAACAAGAAGTACTACATTGATATTGTGGAAGCC

upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ14970 (Selaginella moellendorffii), 3'ss of exon 3
gacttttctaacctttttgaatgtgtggaagtgcatttattttggtatgtgtatttcagtcgttcttttcagccatctaatgtgaacttactgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATATCATGGTTGCTTACAACAATAAGAAGTACTACATTGATATCATTGAATCG
                     |  ||  | ||||    |   | |||  |    | |   |   |||| ||   ||    | |   ||| ||   ||||| |||||||| ||  || |||| || || || || ||  | |||||||| |||||||| || |||||||| ||||||||||||||||||||  | ||| | 
--------------------gtaagta-aggtgccaccagccttgtacttactctgctaacag-ctttccaa--attccgtttcttcttgctt--tgcagATTAGAAACCACGCTGAGGAATTTCTCGTGCCTCACTGTGGGTGACAACATCATGGTGGCGTACAACAACAAGAAGTACTACATTGATATTGTGGAAGCC

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|100385818|gb|BY951012.1|BY951012
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|100406597|gb|BY955683.1|BY955683
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAGATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTANCA-TTGGTGACAATA
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTA-CAATTGGTGACAATA
EST: gi|100418696|gb|BY975696.1|BY975696
EST:     CTTCGGCCCCATACAAAAGATTTTCTGGACATCTCANATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208373274|gb|DC948562.1|DC948562
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208393488|gb|DC949650.1|DC949650
EST:     TTCAGNCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: TTCAG-CCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208387770|gb|DC941339.1|DC941339
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|100415871|gb|BY956965.1|BY956965
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCANATCCAAAGGCTGT                         GTAGGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGT---T-AGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
EST: gi|67508675|gb|BJ941536.1|BJ941536
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTAGGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGT---T-AGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
EST: gi|100448950|gb|CJ973249.1|CJ973249
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208349271|gb|DC906385.1|DC906385
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208346232|gb|DC905221.1|DC905221
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208352262|gb|DC906337.1|DC906337
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTGGAAACTACTTTGCGGAACTTTTCTTGTCTTACGATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208395706|gb|DC920268.1|DC920268
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTNTGCGGAACTTTTCTTGTNTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208366055|gb|DC935844.1|DC935844
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208372135|gb|DC940317.1|DC940317
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208390049|gb|DC938104.1|DC938104
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|100419714|gb|BY957686.1|BY957686
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTAGGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGT---T-AGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
EST: gi|208394989|gb|DC920220.1|DC920220
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTGGAAACTACTTTGCGGAACTTTTCTTGTCTTACGATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208358250|gb|DC930691.1|DC930691
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTAGGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGT---T-AGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACA
EST: gi|208370760|gb|DC948269.1|DC948269
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208357678|gb|DC934130.1|DC934130
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|100442532|gb|BY963226.1|BY963226
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208374165|gb|DC945211.1|DC945211
EST:     CCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTGT                        
genomic: CCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGC--TGTgtaggtgtgc ... ctgggtgca
EST: gi|208374165|gb|DC945211.1|DC945211
EST:     CCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTGT                        
genomic: CCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGC--TGTgtaggtgtgc ... ctgggtgca
EST: gi|208374165|gb|DC945211.1|DC945211
EST:     CCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTGT                        
genomic: CCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGC--TGTgtaggtgtgc ... ctgggtgca
EST: gi|100366066|gb|BY967268.1|BY967268
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCCAAGGCTGT                         GTTAGAAACTACTTTGCGGAAACTTTTCTTGTCCTAACATTTGGTGACAAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAA-CTTTTCTTGTCTTA-CAATTGGTGACAAT
EST: gi|208366022|gb|DC935839.1|DC935839
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAC
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|100386786|gb|BY970327.1|BY970327
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208374981|gb|DC956391.1|DC956391
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208363142|gb|DC954342.1|DC954342
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208356440|gb|DC934430.1|DC934430
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208386327|gb|DC932823.1|DC932823
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
EST: gi|208387581|gb|DC953323.1|DC953323
EST:     CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGT                         GTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT
genomic: CTTCAGCCCCATACAAAAGATTTTCTGGACATCTCAAATCCAAAGGCTGTgtaggtgtgc ... ctgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgtatttcagtcgttcttttcagccatctaatgtgaacttactgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATATCATGGTTGCTTACAACAATAAGAAGTACTACATTGATATCATTGAATCG
                                       aacttac  putative branch site (score: 2)
      tatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttttctaacctttttgaatgtgtggaagtgcatttattttggtatgtgtatttcagtcgttcttttcagccatctaatgtgaacttactgggtgcagGTTAGAAACTACTTTGCGGAACTTTTCTTGTCTTACAATTGGTGACAATATCATGGTTGCTTACAACAATAAGAAGTACTACATTGATATCATTGAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT