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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTTTTTTGGGTTCGGTTCTTGAGGTTGAGAATGGCGACCATCCAGTCAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgacgtctgtgctccttcggaatagtttgtcgaatttcatttacccattgaggaatcggtgcactggtagttgggtcgatgccgattgggtgat...

Basic information

species Physcomitrella patens
transcript PP1S1_526V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os03g14450.1 (Oryza sativa), 5'ss of exon 1
AGAATTTTTTTGGGTTCGGTTCTTGAGGTTGAGAATGGCGACCATCCAGTCAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtg-acgtctgtgctccttcggaatagtttgtcgaatttcatttacccattgaggaatcggtgcactggtagttgggtcgatgccgattgggtgat--
       | |  | | |      |   |   |    |||||||||||||    | ||||| |||   || |  |||||||||||||||||||| |||||||| |   |   |||     || ||| |  |||   ||||       |  | |   ||     |  | ||  ||       | ||   | |  |||| |     
TCCCCGATCTAAGATCCATCCGATCCAGGCCATGGCGGCGACCATCCAGAGCGTGAAGGCCCGCCAGATCTTCGACAGCCGTGGCAACCCCACCGTCGAGgtacgccgcgggtccagtttcgttctgtctagggcgtcgcggcgattgaatcgggtgctttcttagcgcgatgccgc---gatcttggtctgttggttagagc
















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|18331408|gb|BJ163419.1|BJ163419
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162255467|gb|FC431881.1|FC431881
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|100361970|gb|BY947718.1|BY947718
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|18328573|gb|BJ160578.1|BJ160578
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162180206|gb|FC355523.1|FC355523
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|18330497|gb|BJ162503.1|BJ162503
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162275868|gb|FC451429.1|FC451429
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162279243|gb|FC455790.1|FC455790
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|208374338|gb|DC941151.1|DC941151
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|18344784|gb|BJ176825.1|BJ176825
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162255274|gb|FC431584.1|FC431584
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|18349793|gb|BJ181843.1|BJ181843
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|100361603|gb|BY966133.1|BY966133
EST:     GCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: GCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162255040|gb|FC430913.1|FC430913
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|100352733|gb|BY945421.1|BY945421
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162195765|gb|FC371156.1|FC371156
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
EST: gi|162186412|gb|FC362968.1|FC362968
EST:     CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAG                         GCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT
genomic: CAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGT

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: 33 (upstream exon), 35 (downstream exon)
Score: 56

AGAATTTTTTTGGGTTCGGTTCTTGAGGTTGAGAATGGCGACCATCCAGTCAATCAAGGCGCGCGCCATTTATGACAGCCGTGGCAACCCCACTGTCGAGgtgctgtgac ... tgttgaacagGCGGACATCCACTTGTCCGATGGATCGTGGTATCGAGCTGCAGTGCCCAGTGGTGCTTCCACTG




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