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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGGGCAAGGAGAGGGGATGGCCCAACGCTGATCGAATGTGAGACATACCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttcacccttatcattctgctctcatctagaggcaaactcggataattttattcttgttagttagtttcgttcccgtttaccttaatctctcaagaaatatggtaactgtcttcgtgtttttctctttacttatttatttatttattgatttgcag

Basic information

species Physcomitrella patens
transcript PP1S318_24V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S318_24V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G033894_T01 (Zea mays), 5'ss of exon 2
GAGAGGGCAAGGAGAGGGGATGGCCCAACGCTGATCGAATGTGAGACATACCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttcacccttatcattctgctctcatctagaggcaaactcggataattttattcttgttagttagtttcgttcccgtttaccttaatctctcaagaaatatggtaactgtcttcgtgtttttctctttacttatttatttatttattgatttgcag
||||||||||||||||| || || ||||| ||  |||| ||||| |||||| ||||| |||||||||| ||||| || ||||| || ||  || ||||||||||   | ||  |  |  ||  |||    | |      |     |      || ||      |  |   | | ||          || | |  ||  ||||||                                                         
GAGAGGGCAAGGAGAGGTGAAGGGCCAACCCTAGTCGAGTGTGAAACATACAGGTTCCGGGGTCACTCCCTTGCAGACCCAGATGAGCTCAGGAAGCCTGgtaaggattactttcct-gtttggct---gtttcattttatttctgttctgcttcataaagaatgatgtttctggtatgaaccaggctaactgactggagaaat---------------------------------------------------------
















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|37829190|gb|BJ587202.1|BJ587202
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|208363373|gb|DC946971.1|DC946971
EST:     CCGGTTCAGGGGTCATTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162154669|gb|FC331607.1|FC331607
EST:     GGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: GGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162158060|gb|FC334461.1|FC334461
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|208390105|gb|DC945968.1|DC945968
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162270268|gb|FC447280.1|FC447280
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162170267|gb|FC346464.1|FC346464
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162170268|gb|FC346465.1|FC346465
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162190014|gb|FC366588.1|FC366588
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162270267|gb|FC447279.1|FC447279
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
EST: gi|162181806|gb|FC357405.1|FC357405
EST:     CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTG                         CTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT
genomic: CCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGT

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: 13 (upstream exon), 23 (downstream exon)
Score: 2

GAGAGGGCAAGGAGAGGGGATGGCCCAACGCTGATCGAATGTGAGACATACCGGTTCAGGGGTCACTCACTTGCCGATCCAGACGAACTTCGGGAGCCTGgtaattttca ... tgatttgcagCTGAGAAAGCACATTACGCTGCGAGGGACCCGATTGTTGCCCTAAAGAAGTATCTGCTAGAGAACGAGATAGCTACTGAAGCTGAATTGAAGACCATTGA




<











<


<