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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT

Basic information

species Physcomitrella patens
transcript PP1S306_43V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT
                                                                                                    | | |    ||    |   | | |  || | | |  ||    ||||||  |       ||      | |   || ||||| ||||    || ||||||||||||||||| |||||  | ||||||||| | || |||||||| |||||| |||| ||||  |||
--------------------------------------------------------------------------------------------------gttggtggatctctaattccatagcactttagttctacactgatgtaaccttctcacaaaat------ttttccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT
                                                                                    ||   || ||   || |  |    || ||| ||| ||   |  |  | | | | || | | ||  || |    || |   |||    |   || || ||||    || ||||||||||||||||| |||||  | ||||||||||| ||||||||||| ||||| ||||| ||||  |||
------------------------------------------------------------------------------------gttaggg-atctctaatctc---tgtggtgtttttttcatt--tcagctgtaatga-gttgacaagc-tcacctaagtttgattctcg---tgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT
                                                                                               ||| |||   |   |||  | |   |   || || || |    |     ||  |   |||  | | ||  || |     || ||| |||||||||| || ||||||||||||||||| ||| | || ||||| |||||||||||||| ||||| || || ||||  || 
-----------------------------------------------------------------------------------------------gtttgttaaata-atcgcaggtgcctctttggtgcgtgtgcttgtt--caaatgaaatttaatgtagc--atataactctt-cagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 10
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgt-cgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT
                                                                                    |||   | | |   |||    ||| |   | |||||||   | |    | ||  |     |         ||  |||    | ||         ||| | ||||| ||||||||||| || ||||| ||||| ||||| ||||| || || ||||||||||| ||||| |||||||  |||
------------------------------------------------------------------------------------gtactagaaatcaaagtaa-atgcatatatagtttgtt---tctctcatcttatcataaatttttatttattcatatccttgttgc--------cagATATTCCATAAACGCATGCCTCCAGAAGCTGTTGATTTGGTTTCAAGACTACTGCAGTACTCTCCTAATCTACGGTGCACAGCT

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT
                                                                                                      |   | |   |  |  | |  || |     | || |            |  ||| | ||||   |       |  |||||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||||| || || |  || || ||||| || 
------------------------------------------------------------------------------------------------------gtaagagcaatcatccggtatatctctctctctgtct-----------ctcttgatgtggctcgt-------tgacagGTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC

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|100389546|gb|BY989024.1|BY989024
EST:     ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA                         GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
genomic: ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttt ... ggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
EST: gi|37823641|gb|BJ581707.1|BJ581707
EST:     ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA                         GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
genomic: ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttt ... ggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
EST: gi|100449000|gb|CJ973299.1|CJ973299
EST:     ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA                         GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
genomic: ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttt ... ggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
EST: gi|18338380|gb|BJ170404.1|BJ170404
EST:     ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA                         GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC
genomic: ACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttt ... ggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT
               cggtaac  putative branch site (score: 3)