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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgcaaatgtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA

Basic information

species Physcomitrella patens
transcript PP1S12_267V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgcaaatgtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA
                                                        | |  |   |       | | ||||      ||   | |    |  | |   ||||   || |    | || | |   | |  |     |    | |||||||||| ||||| |||||||||||  | ||||| ||||| ||||| ||  | ||||| ||||||||||| || || ||||| ||  | |
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgt-taacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgcaaa------------tgtggtt-acagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA
                         ||| ||  ||||    ||   | |||  |  |||    ||| || | ||||| |  |  ||||             | || || | |||||||| || ||||||||||||||| |||||||||| || || || ||| | ||||| ||||||||  |  | || || || || || |
-------------------------gtgagaacaatgt---tacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
-tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgc--aaatgtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA
 |  | ||||   |  |   || | | | | ||        ||| | | ||   ||   |||| |     | |||||  | ||  ||  ||||    | |||||||||| || || |||||  ||||| ||||||||||||| ||||||||| | ||||| || ||||| || || || ||||| ||  |||
gtaagatcttg-agcctctttcaattttcgaatactgaagaataacattgcagatcattttttga-----tgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA

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|162197427|gb|FC372805.1|FC372805
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
EST: gi|100364148|gb|BY966739.1|BY966739
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
EST: gi|162171600|gb|FC347541.1|FC347541
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGA
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGA
EST: gi|100445813|gb|CJ970112.1|CJ970112
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
EST: gi|208387491|gb|DC933354.1|DC933354
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggcttctctcctttttactgacttattaatgttgattgcaaatgtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA
                        ttattaatgttgatt  TA-rich tract