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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgtttgcttaatggtatctagtcaatgtcatgtgaaacttcgcaacctttgcttctagcttggtgttttttttctgatcactttgttgtaatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGGACGCATTGCCATCGCTGCGGCTTAGTTACATGAATGTAGCAGTAGTACT

Basic information

species Physcomitrella patens
transcript PP1S84_153V6.1
intron # 3
splice site 3'
intron type U2

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|162242036|gb|FC419409.1|FC419409
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162209398|gb|FC385513.1|FC385513
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162200859|gb|FC377054.1|FC377054
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|18344903|gb|BJ176944.1|BJ176944
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162200093|gb|FC376555.1|FC376555
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162240450|gb|FC416016.1|FC416016
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|19788851|gb|BQ040961.1|BQ040961
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162200888|gb|FC377083.1|FC377083
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|19781146|gb|BQ039660.1|BQ039660
EST:     CCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGNAAGGATGTTACGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCG
genomic: CCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAG-AAGGATGTTA-GGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCG
EST: gi|162199841|gb|FC376707.1|FC376707
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|37824109|gb|BJ582175.1|BJ582175
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|67726367|gb|BJ976626.1|BJ976626
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162204915|gb|FC380597.1|FC380597
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACTTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|19786736|gb|BQ040532.1|BQ040532
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162239228|gb|FC416497.1|FC416497
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162214855|gb|FC390990.1|FC390990
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162200860|gb|FC377055.1|FC377055
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|67717860|gb|BJ968119.1|BJ968119
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162246164|gb|FC423600.1|FC423600
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|7047316|gb|AW477210.1|AW477210
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162274330|gb|FC450298.1|FC450298
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         C--AAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162200092|gb|FC376554.1|FC376554
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162204916|gb|FC380598.1|FC380598
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|7207529|gb|AW561528.1|AW561528
EST:     TGCCTGAAGCAGCTGGAGGCTCTTAACATAATCAAGAAGGATGTTAGGGG                         AGGAAGGCGCATGACCTGTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162218915|gb|FC394861.1|FC394861
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162214237|gb|FC390283.1|FC390283
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|18340129|gb|BJ172157.1|BJ172157
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162276832|gb|FC452514.1|FC452514
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|7207470|gb|AW561471.1|AW561471
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAATCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAAGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|15327019|gb|BI487480.1|BI487480
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
EST: gi|162236411|gb|FC412778.1|FC412778
EST:     TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGG                         AGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG
genomic: TGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGG

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: 35 (upstream exon), 35 (downstream exon)
Score: 135

GAGTTAGACCGTCTCACTTTGCCAAGAGCAGCGGTTCAATTGCAAGGCACTGCCTGAAGCAGCTAGAGGCTCTTAACATAGTCGAGAAGGATGTTAGGGGgtcagttcct ... taatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGGACGCATTGCCATCGCTGCGGCTTAGTTACATGAATGTAGCAGTAGTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctttgcttctagcttggtgttttttttctgatcactttgttgtaatttgcagAGGAAGGCGCATCACCTCTGATGGGCAGCGTGACCTTGATCAGGTAGCCGGACGCATTGCCATCGCTGCGGCTTAGTTACATGAATGTAGCAGTAGTACT
                            ttctgat  putative branch site (score: 135)
                    tgtttttttt  TA-rich tract