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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttcttatttaaaaaagcctcaacgggtgcttcaacactaaggagagtagaatactgttttagcatgtttttgagaactgtataacatatctttc...

Basic information

species Physcomitrella patens
transcript PP1S175_129V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S175_129V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 2
ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgt-agttttcttatttaa-aaaagcctcaacgggtgctt-caacactaaggagagtagaatactgttttagcatgtttttgagaactgtataacatatctttc-
 | || |||||  | || ||  |    ||  |||||||  | ||||||||||| ||||||||||||||||| || ||||| ||||| || | |  | |  || | ||   ||     |  | |  ||  |          || |||   | ||| ||     |    |  |  | |||       |  
GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctctagtctacaacataaagatcggtttgcacctgtaatccagtactcgaaagcatatattcttaacaa----tcagaagttagacaacgggagcatgg
















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|100446650|gb|CJ970949.1|CJ970949
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|162231926|gb|FC408792.1|FC408792
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|100429680|gb|BY959684.1|BY959684
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCAAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|162223327|gb|FC400569.1|FC400569
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|18349218|gb|BJ181267.1|BJ181267
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|100437874|gb|BY961539.1|BY961539
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|100353475|gb|BY964825.1|BY964825
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
EST: gi|18357672|gb|BJ189731.1|BJ189731
EST:     ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG                         GTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA
genomic: ACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCA

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: 28 (upstream exon), 35 (downstream exon)
Score: 6

ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAGgtagttttct ... gctttggcagGTCTTGGAAGCGCTGGGCAGCATGGAGTTTCCAAACATTTATCCTGACCCAGAAAGTCGCAGGTTGAGGGCTGCACTAGCTGAGGATACAGGAATAGGAG




<











<


<