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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccgtcattgtgctgaatgcttctattagcaatctcttcattctttgttgtgtgaacagttgagtttcgaaattatattctgttcttcgaaatg...

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_197V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: EFJ29519 (Selaginella moellendorffii), 5'ss of exon 12
ACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccgtcattgtgctgaatgcttctattagcaatctcttcattctttgttgtgtgaacagttgagtttcgaaattatattctgttcttcgaaatg
  | || || |  || || || || ||||||||||||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||  | || ||||  |       | | |  ||  ||    || | | ||  |   || ||| || | |      |||  | | | |                       
CTTGGGAGACGCCGGCCGAGCAGCCATTCAAACGCAAGGCTCGGTTAGCAATCCGTTCGGGCCAACCTTCGTCTATGGCTACCGAAACATCGCATTTGAAgtaacca-------tattcccaagtctctctttggaactcagtgtgtttttttttttct------ttgtttcttgtag----------------------

upper sequence: PP1S58_197V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: EFJ28090 (Selaginella moellendorffii), 5'ss of exon 12
ACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccgtcattgtgctgaatgcttctattagcaatctcttcattctttgttgtgtgaacagttgagtttcgaaattatattctgttcttcgaaatg
  | || || |  || || || || ||||||||||||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||  | || ||||  |       | | |  ||  ||    || | | || ||   || |||  |   |      |||  | | |                         
CTTGGGAGACGCCGGCCGAGCAGCCATTCAAACGCAAGGCTCGGTTAGCAATCCGTTCGGGCCAACCTTCGTCTATGGCTACCGAAACATCGCATTTGAAgtaacca-------tattcccaagtctctctttggaactcactatgtttttttcttctttgtttcttgtatgtag-------------------------
















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|67701566|gb|BJ961799.1|BJ961799
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|208382909|gb|DC928334.1|DC928334
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|67726513|gb|BJ976772.1|BJ976772
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|37823222|gb|BJ581288.1|BJ581288
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|37836886|gb|BJ594894.1|BJ594894
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|208370963|gb|DC944338.1|DC944338
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|162176258|gb|FC352715.1|FC352715
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|18337725|gb|BJ169749.1|BJ169749
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|37842901|gb|BJ600909.1|BJ600909
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|162155578|gb|FC331529.1|FC331529
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
EST: gi|37821349|gb|BJ579415.1|BJ579415
EST:     ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAG                         GTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG
genomic: ATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATG

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: 21 (upstream exon), 30 (downstream exon)
Score: 15

ACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTCTGGAGgtaattaccg ... gacttcacagGTAATGAAGAATGGGCATATTGCAACTGTGACTCTCTTCCAGAGCACCATGTAAAGTCGTACAACACTACAGGACATTGCTTTAGTCGTGCTCATTGCCC




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