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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGGAATGAAAGGCGCTGTCCAAAAAGCAGAAGAAATTGTGAAGAAAACTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatcgcacacatagctgaattcagtattaccactgatcttttcagaactttccttacaactgataattttttaatcttactttctttgcaactgcgaatcttaatcttgtttcggtagaaggaagagttagctgatccatgtgtatgtcgtgtag

Basic information

species Physcomitrella patens
transcript PP1S17_59V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S17_59V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ24611 (Selaginella moellendorffii), 5'ss of exon 3
TAAGGGAATGAAAGGCGCTGTCCAAAAAGCAGAAGAAATTGTGAAGAAAACTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcaca-tcgcacacatagctgaattcagtattaccactgatcttttcagaactttccttacaactgataattttttaatcttactttctttgcaactgcgaatcttaatcttgtttcggtagaaggaagagttagctgatccatgtgtatgtcgtgtag
 || || |||||||| || || || ||||| || || ||  ||||||| ||||| || || ||||||||||||||||| || ||||| |||||||| |||||     | | |      || | || || |  | | |   |   | ||||||                                                                                                              
GAAAGGCATGAAAGGAGCAGTACAGAAAGCCGAGGAGATATTGAAGAAGACTCCAAATTCTTACATGCTCCAACAATTTGAAAACCCCGCAAATCCCAAGgtgcgttagttgtctctttatccgagtttaacactcctttta--cgtttcag--------------------------------------------------------------------------------------------------------------

upper sequence: PP1S17_59V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ13264 (Selaginella moellendorffii), 5'ss of exon 3
TAAGGGAATGAAAGGCGCTGTCCAAAAAGCAGAAGAAATTGTGAAGAAAACTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcaca-tcgcacacatagctgaattcagtattaccactgatcttttcagaactttccttacaactgataattttttaatcttactttctttgcaactgcgaatcttaatcttgtttcggtagaaggaagagttagctgatccatgtgtatgtcgtgtag
 || || |||||||| || || |||||||| || || ||  ||||||| ||||| || || ||||||||||| ||||| || ||||| |||||||| |||||     | |        || | || || |  | |    ||  || ||||||                                                                                                              
GAAAGGCATGAAAGGAGCAGTACAAAAAGCCGAGGAGATATTGAAGAAGACTCCAAATTCTTACATGCTCCAGCAATTTGAAAACCCCGCAAATCCCAAGgtgcgttagttatctctttatccgagtttaacactc---cttttcgtttcag--------------------------------------------------------------------------------------------------------------
















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|162268500|gb|FC444373.1|FC444373
EST:     AGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACT-GACCCAGAGATTTGGGAAGATACAGCCGGAAA
genomic: AGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGA-CCAGAGATTTGGGAAGATACAGCCGGAAA
EST: gi|208377588|gb|DC922691.1|DC922691
EST:     CCAGCAAATCCTAAG                         GTTCANTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|67728207|gb|BJ978466.1|BJ978466
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|162263267|gb|FC438555.1|FC438555
EST:     ATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: ATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|67727983|gb|BJ978242.1|BJ978242
EST:     CAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|162263268|gb|FC438556.1|FC438556
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|100389151|gb|BY952355.1|BY952355
EST:     TCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAAG                         GT-CATTTTGAGACTACTGGACC
genomic: TCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAA-Ggtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACC
EST: gi|67574856|gb|BJ947680.1|BJ947680
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACC
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACC
EST: gi|162216431|gb|FC393264.1|FC393264
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|100364747|gb|BY947888.1|BY947888
EST:     CTCCCA-CTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCCGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|162219191|gb|FC396630.1|FC396630
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|208395218|gb|DC916027.1|DC916027
EST:     TCATACATGTTCC-ACAATTCGAGAACCCAGCAAATCCTNAG                         GTTCA-TTTGAGACTACTGGACCAGAGA-TTGGGAAGATACAGCCGGAAAA
genomic: TCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|162150189|gb|FC326066.1|FC326066
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|208349136|gb|DC902170.1|DC902170
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|162154236|gb|FC330367.1|FC330367
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|100352878|gb|BY945495.1|BY945495
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGAC
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGAC
EST: gi|162164732|gb|FC340779.1|FC340779
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|162278511|gb|FC453973.1|FC453973
EST:     AGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: AGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|100359503|gb|BY947020.1|BY947020
EST:     TCCCAACTCATACATGCTCCAAACA-TTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAG
genomic: TCCCAACTCATACATGCTCCAA-CAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAG
EST: gi|162277367|gb|FC453173.1|FC453173
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|100410588|gb|BY992174.1|BY992174
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGGAAA
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|67728189|gb|BJ978448.1|BJ978448
EST:     CTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
genomic: CTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAA
EST: gi|100392796|gb|BY971888.1|BY971888
EST:     TCCCAACTCATACATGCTCCCAACA-TTCGAGAAACCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATAC
genomic: TCCCAACTCATACATGCTCC-AACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATAC
EST: gi|18356110|gb|BJ188169.1|BJ188169
EST:     CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGAC
genomic: CTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGAC
EST: gi|67697830|gb|BJ958063.1|BJ958063
EST:     CCAGCAAATCCTAAG                         GTTCATTTTGAGACTACTGGACCAGAGATTTGGGAANGATACAGCCGGAAA
genomic: CCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAA-GATACAGCCGGAAA

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: 62

TAAGGGAATGAAAGGCGCTGTCCAAAAAGCAGAAGAAATTGTGAAGAAAACTCCCAACTCATACATGCTCCAACAATTCGAGAACCCAGCAAATCCTAAGgtatcacatc ... tgtcgtgtagGTTCATTTTGAGACTACTGGACCAGAGATTTGGGAAGATACAGCCGGAAAAATTGACATTCTTGTTGCTGGCATTGGTACCGGTGGAACTGTAACTGGAG




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