Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcatcgaagtttttcagggccattgacgtttagctcttggttttcgtgacgcctttccttggcgtggtattcacaagtgatttggatttatttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAGACCCCCAAGGCTTACCGCATGAAGTTGTGGGCCACGGACGAAGTGCGCG

Basic information

species Physcomitrella patens
transcript PP1S44_13V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_13V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G10220.1 (Glycine max), 3'ss of exon 1
cgcatcgaagtttttcagggccattgacgtttagctcttggttttcgtgacgcctttccttggcgtggtattcacaagtgatttgg-atttatttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAGACCCCCAAGGCTTACCGCATGAAGTTGTGGGCCACGGACGAAGTGCGCG
         ||   | ||   ||    | ||| |   | | |||   |  |  || |   ||   |  ||       ||| ||||  || | | ||| ||||||||||||||||||||||||||| | || ||||| ||    |   || ||  |||||||   ||||| |||||| | ||||||||  |||| || ||||
---------gtgcgtaagattcac-accatttggtgttcgatttcattttcctctgttaatgatttt-tacgaggtggtgttttgttatgtgtatttgcagTTTCACCAGTACCAGGTGGTTGGGAGGGCTCTTCCCACGGAAGCAGATCAGCACCCCAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG

upper sequence: PP1S44_13V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
-----cgcatcgaagtttttcagggccattgacgtttagctcttggttttcgtgacgcctttccttggcgtggt-attcacaagtgatttggatttatttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAGACCCCCAAGGCTTACCGCATGAAGTTGTGGGCCACGGACGAAGTGCGCG
     |   ||     |||||  ||| |   |     ||   | ||| ||  | |     |||||     |  | ||||  || ||  || | ||        ||||||||||||||||||||||| ||| | ||||||||  |        |||||   || | |   ||| | |||||| | ||||| ||| |||| || || |
tttttcttttcctgaattttctcggcaaccaa-acaaaggaataggtgtt--ttatttaattcctgaatctattgattctgaaatgggttcgtttgggc---gcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
















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|162266174|gb|FC441716.1|FC441716
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162266175|gb|FC441717.1|FC441717
EST:     TCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGTATCTTCCGAG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGA
genomic: TCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATG-ATCTTCCG-Ggttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGA
EST: gi|208396096|gb|DC924562.1|DC924562
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATNTTCCGG                         TTTCACCANTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67696679|gb|BJ956912.1|BJ956912
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|18357574|gb|BJ189633.1|BJ189633
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|18350689|gb|BJ182740.1|BJ182740
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67709657|gb|BJ965473.1|BJ965473
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|7584115|gb|AW700012.1|AW700012
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|37851559|gb|BJ609567.1|BJ609567
EST:     GTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCCGGGCAATGA
genomic: GTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAA-CCCCGGGCAATGA
EST: gi|67697357|gb|BJ957590.1|BJ957590
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162240668|gb|FC416286.1|FC416286
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162245994|gb|FC421883.1|FC421883
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|18373717|gb|BJ205295.1|BJ205295
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|208395723|gb|DC924217.1|DC924217
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67573969|gb|BJ946793.1|BJ946793
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|37822679|gb|BJ580745.1|BJ580745
EST:     GTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: GTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162231453|gb|FC407903.1|FC407903
EST:     GCTTTGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: GCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162210802|gb|FC387212.1|FC387212
EST:     ACTCCTCCGCTTTGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162210803|gb|FC387213.1|FC387213
EST:     CTCNCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: CTC-CTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67572452|gb|BJ945276.1|BJ945276
EST:     ACTCCTCCGCTTCGTACCCNTTATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|37844205|gb|BJ602213.1|BJ602213
EST:     ACTCCTCCGNTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67573294|gb|BJ946118.1|BJ946118
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67695825|gb|BJ956058.1|BJ956058
EST:     TACCCACAATTTTTATCAGCAGCCTATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCANCCCCGGGCAATGAG
genomic: TACCCACAATTTTTATCAGCAGCC-ATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|208372673|gb|DC944638.1|DC944638
EST:     ACCCACAATTNTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|67723733|gb|BJ973992.1|BJ973992
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|6167152|gb|AW145416.1|AW145416
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|18371390|gb|BJ202992.1|BJ202992
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162253146|gb|FC428978.1|FC428978
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|162260866|gb|FC438222.1|FC438222
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|208349310|gb|DC910383.1|DC910383
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|18372435|gb|BJ204037.1|BJ204037
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
EST: gi|18343483|gb|BJ175521.1|BJ175521
EST:     ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGG                         TTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG
genomic: ACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAG

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: 32 (upstream exon), 35 (downstream exon)
Score: 42

AGCCTCTTCCATTCCTCCTCGTTGTTGGAACCCTGCACTCCTCCGCTTCGTACCCACAATTTTTATCAGCAGCCATGATCTTCCGGgttcgtatcc ... atttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAGACCCCCAAGGCTTACCGCATGAAGTTGTGGGCCACGGACGAAGTGCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgacgcctttccttggcgtggtattcacaagtgatttggatttatttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAGACCCCCAAGGCTTACCGCATGAAGTTGTGGGCCACGGACGAAGTGCGCG
                                          tttattttt  CT-rich tract
                                   atttggatttattttt  TA-rich tract