Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgaagaggacttgctcactcgtgcgctcgcctcgtcgtcgtctgtttatttttgtcaaaaacattaattcgtttggtttttttgcctatgcctgctttgactgaaaatttgcttaacgtgctaaatgaagttagctttgtacgtgcggcctaagacatatgggtttgtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG

Basic information

species Physcomitrella patens
transcript PP1S19_94V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
gttagtgaagaggacttgctcactcgtgcgctcgcctcgtcgtcgtctgtttatttttgtcaaaaacattaattcgtttggtttttttgcctatgcctgctttgactgaaaatttgcttaacgtgctaaatgaagttagctttgtacgtgcggcctaagacatatgggtttgtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG
                                                     |  |||   |   | | ||||    ||| |   |||  |     |  |   |||     |||  || |    || |||||   || |  |            |  | ||||||          ||||||||| || || ||| | || || || |||||||| || ||||| ||||||||||| ||| | || ||||| || ||||| ||||||||||||
-----------------------------------------------------tacttgatgaggtcctaaatt----tggataccttgttttcaattcttacaact-----tttcttttat---cttaatgattctaacact-------tattttttgtcatatga---------tgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG

upper sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 2
gttagtgaagaggacttgctcactcgtgcgctcgcctcgtcgtcgtctgtttatttttgtcaaaaacattaattcgtttggtttttttgcctatgcctgctttgactgaaaatttgcttaacgtgctaaatgaagttagctttgtacgtgcggcctaagacatatgggtttgtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG-
                                                       ||  |   |     |||   ||||||||   |||  |     |  |   |||     |||  || |    || |||||   |  ||     |   |    |  | ||||||          ||||||||| || || ||| | || || || |||||||| || ||||| ||||||||||| ||| | || ||||| || ||||| |||||||||||| 
-------------------------------------------------------ttcat--gaggtcctaa---gtttggttaccttgttttcaattcttacaact-----tttcttttat---cttaatgattcttact-----cactcattttttgtcatatga---------tgcaggTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAGG
















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|208397640|gb|DC912258.1|DC912258
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100401165|gb|BY990863.1|BY990863
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|208399535|gb|DC908532.1|DC908532
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100444887|gb|BY982715.1|BY982715
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100418660|gb|BY957527.1|BY957527
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100421604|gb|BY976229.1|BY976229
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100413766|gb|BY974978.1|BY974978
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|208359964|gb|DC939296.1|DC939296
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGGCAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100434157|gb|BY978986.1|BY978986
EST:     GTATCCGGTGCCTAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100380032|gb|BY968812.1|BY968812
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100449796|gb|CJ973940.1|CJ973940
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100426311|gb|BY958834.1|BY958834
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100417096|gb|BY957165.1|BY957165
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|208352244|gb|DC901737.1|DC901737
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100355920|gb|BY946105.1|BY946105
EST:     GTATCCTGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGTGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100450661|gb|CJ974375.1|CJ974375
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|208359017|gb|DC957765.1|DC957765
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGGCAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|208383715|gb|DC911453.1|DC911453
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100446804|gb|CJ971103.1|CJ971103
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100385991|gb|BY951185.1|BY951185
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
EST: gi|100446201|gb|CJ970500.1|CJ970500
EST:     GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCG                         GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA
genomic: GTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTA

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), 26 (downstream exon)
Score: 3

ATGGAAGCTACGGCGGCAGCTCATTTCTCTGGCCTGCACTTTGACGATGAGTATCCGGTGCCGAAGTACAAAGGCGCTGACAAGGTCCCCTTCGTCATCGgttagtgaag ... gtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatgaagttagctttgtacgtgcggcctaagacatatgggtttgtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG
 tgctaaa  putative branch site (score: 3)