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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaaggaccggaatctgtcgtttcaataattcattgtcctttttctgaagatcggaacgacagaaatctcactccgttcacgtcgtattgtatggcagGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTGACTAAAGGTGATCAGTATGATGTACGAGAACAATCTTCAGCACGTGAG

Basic information

species Physcomitrella patens
transcript PP1S43_232V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 9
ttgaaaggaccggaa----tctgtcgtttcaa--taattcat-tgtcctttttctgaagatcggaacgacagaaatctcactccgttcacgtcgtattgtatggca-gGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTGACTAAAGGTGATCAGTATGATGTACGAGAACAATCTTCAGCACGTGAG
 | | ||    ||||    |||   | || ||  || || || ||| |||   ||   |   | |   |     || |   |    | ||     ||||| |   | ||| ||||| ||||| |||||  |||  || ||    |||||||||||||| || ||||| || |||||||||||| |||||||  |   ||    ||||
gtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctggggtgcattcatt---attttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG

upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 9
ttgaaaggaccggaa----tctgtcgtttcaa--taattcat-tgtcctttttctgaagatcggaacgacagaaatctcactccgttcacgtcgtattgtatggca-gGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTGACTAAAGGTGATCAGTATGATGTACGAGAACAATCTTCAGCACGTGAG
 | | ||    ||||    |||   | || ||  || || || ||| |||   ||  ||   | |   |     || |   |    | ||     ||||| |   | ||| ||||| |||||||||||  |||  || ||    |||||||||||||| || ||||| || |||||||||||| |||||||  |   ||    ||||
gtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctagggtgcattcatt---attttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTTGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
















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|100372791|gb|BY948705.1|BY948705
EST:     GCCTGTCCAAAGAACGTATCCACAAGCCAGCCTCTTCACTTGCAAAACGG                         GTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTG
genomic: GCCTGTCCAAAGAACGTATCCACAAGCCAGCCTCTTCACTTGCAAAACGGgtacgggtgc ... tgtatggcagGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTG
EST: gi|162240842|gb|FC417513.1|FC417513
EST:     GCCTGTCCAAAGAACGTATCCACAAGCCAGCCTCTTCACTTGCAAAACGG                         GTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTG
genomic: GCCTGTCCAAAGAACGTATCCACAAGCCAGCCTCTTCACTTGCAAAACGGgtacgggtgc ... tgtatggcagGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaagatcggaacgacagaaatctcactccgttcacgtcgtattgtatggcagGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTGACTAAAGGTGATCAGTATGATGTACGAGAACAATCTTCAGCACGTGAG
                      atctcac  putative branch site (score: 3)
                                          tattgtat  TA-rich tract