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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatgaaagcgacaaaactttatgtgtattctgctcaagtatgtggtccaacttgcattaagtgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA04G08560.1 (Glycine max), 3'ss of exon 10
----acacatgaaagcgacaaaactttatgtgtattctgctcaagtatgtggtccaacttgcattaagtgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA
            |  |   |  |  |||  | | ||||  | |  | |||  |      | |||| | ||   |  |     ||| || ||  ||      ||||||||||||| ||||||| |||| || | ||||||||||||||||| |||||||| ||||||||   |   |||||    ||||||||     | || ||
acttgtttgctcattctttaccatcttac-tctgttctttttagttttgtt-tttgtgatacatttactgcagttataataatttctcctt--taactggtcagGCACACCTGGTGATTGGAGTCACATTATCAAGCAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTACCA

upper sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 9
acacatga--aagcgacaaaactttatgtgtattctgctcaagtatgtggtccaact-tgcattaagtgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA
     |||  |  |   |  |  |||  | | ||||    |  | | || |       | | || | |  |  | | | ||  |||||    ||      ||||||||||||||||||||| |||| || | || |||||||||||||| |||||||| ||||||||   |   |||||    ||||||||     | |  ||
ttgtttgatcattctttactatcttac-tctgttctttctagttttctgtttttgtgatacgtttatt--tcagttatattgatttctcctttaactggtcagGCACACCTGGCGATTGGAGTCACATTATCAAACAGATTGGAATGTTTACTTTCACTGGATTGAATGCGGAACAAGTTTCCTTCATGACTAAAGAGTTCCA

upper sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 10
acacatgaaagcgacaaaactttatgtgt---attctgctcaagtatgtggtccaacttgcattaagtgatttggtc----tctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA
      |||||| | | || |  ||  ||   | |  | |  |  |  |    |  |||| | | | |  |   | |    |   | || ||||| | ||   ||||||||||| || || |||| |||| |||| ||||||||||||||||| |||||||| ||||||||||   ||||||| |  |||||||||    | || ||
------gaaagcaatagaagtgcataagttcaaatagggtgcataacatttatcttcttgaactgaattctcatgccagaatgcatcttcctttggtgtttg-gcagGCACACCAGGTGACTGGAATCACATTCTCAAGCAGATTGGAATGTTTACTTTCACAGGATTGAACACCGCTCAAGTGGCCTTCATGACCAAAGAGTACCA

upper sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv11s0016g03720.t01 (Vitis vinifera), 3'ss of exon 10
--acacatgaaagcgacaaaactttatgtgtattctgctcaagtatgtggtccaacttgcattaag---tgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA
       ||   |       |||||   || |||     || ||   |  |     ||| ||||||   ||  || |  | | ||| |||||  ||||   |||||||| |||||||| |||| |||| || | ||||| |||||||||||||||||||| ||  |||| |     |||||||  |||||||||    |||||||
tcttttgtggttgttcatgtactttgaatgaatttc---catgttaataattgtgtttg-attaagaattgtgtttggatttatttctctttcctatttg-gcagGCACCCCTGGCGACTGGAGTCACATTATAAAGCAAATTGGAATGTTCACTTTCACAGGGCTGAATACTGAGCAAGTCGCCTTCATGACCAAGGAATATCA

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|208348540|gb|DC905819.1|DC905819
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|208385027|gb|DC919707.1|DC919707
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162173605|gb|FC349573.1|FC349573
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162182166|gb|FC358181.1|FC358181
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|67726923|gb|BJ977182.1|BJ977182
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|37831224|gb|BJ589236.1|BJ589236
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|37851862|gb|BJ609870.1|BJ609870
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162196336|gb|FC375406.1|FC375406
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|37839276|gb|BJ597284.1|BJ597284
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|208400819|gb|DC925099.1|DC925099
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACNTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162267155|gb|FC443386.1|FC443386
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|208350485|gb|DC926452.1|DC926452
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|67699338|gb|BJ959571.1|BJ959571
EST:     GCTCTGCAAGCTCGAG                         GCACACCTGGCGATNGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: GCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162205457|gb|FC381555.1|FC381555
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162196335|gb|FC375405.1|FC375405
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162173604|gb|FC349572.1|FC349572
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|208366377|gb|DC947573.1|DC947573
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162175651|gb|FC351238.1|FC351238
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162263808|gb|FC438427.1|FC438427
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACCT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|37842485|gb|BJ600493.1|BJ600493
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
EST: gi|162176138|gb|FC351087.1|FC351087
EST:     TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG                         GCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT
genomic: TCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTT

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: 14

GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAGgtgtgtggtt ... attcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtccaacttgcattaagtgatttggtctctttttttctttgatattcatgcagGCACACCTGGCGATTGGACTCACGTTCTGAAGCAGATTGGAATGTTCACTTTCACGGGATTGAACAAGTCTCAAGTCGAGTTCATGACCCGTCAATATCA
                                      ctttgat  putative branch site (score: 14)
                           tctctttttttctttg  CT-rich tract
                               tttttttctttgatat  TA-rich tract