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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctggccctccgaacttatctcatgcatttgtctgcttaacacttccaacattattcatcaattcagtcacctgactctttcagggcttatgtg...

Basic information

species Physcomitrella patens
transcript PP1S81_234V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S81_234V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G104920_T03 (Zea mays), 5'ss of exon 12
GAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctggcc----ctccgaacttat-ctcatgca-tttgtctgcttaacactt-----ccaacattattcatcaattcagtcacctgactctttcagggcttatgtg
 ||||||||||  ||||| ||||||||||| ||  || |||| |||| ||||||| ||||||| || |||||  | || ||||| ||||| ||||| |||||| ||||  ||       | |  | | | | ||||||   ||  |  |||  |  |      ||| || ||  ||||  |  ||  ||| |||||  ||  | ||     
CAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTGTTTATCACAAGgtaatggcaagcttctgtcctggtcatgttcccatgcagcatgcattgttatgatgtgtgactcaatataatcaatcagatgggtt-cctaactcta-cactgattgcag-

upper sequence: PP1S81_234V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 12
GAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgt----attggctggccctc---cgaacttatctcatgcatttgtctgcttaacacttccaacattattcatcaattcagtcacctgactctttcagggcttatgtg
 ||||||||||| |||||||||||||| ||||| ||  |||| |||||||||||| || |||| || |||||| | ||||| ||||| || || ||||||||    | |  |||  | |    |   |   | ||||||||||  ||  |  | |||   ||    |||    | |      |    || |||| |    ||     
CAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCGTCTACCATAAGgttagtagtacctgatcttaaaacagccaattttcatgcattttactatt--atactaagaat-ccatttgatagtaattctaggaaacgcttttactatttt----

upper sequence: PP1S81_234V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 12
GAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctggccctccgaacttatctcatgcatttgtctgcttaacacttccaacattattcatca-attcagtcacctgactctttcagggcttatgtg
 | ||| ||  | || |||||||||||||| ||  |||| || ||||| || ||  |||| |||||||||||| ||||||| ||| | |||||||| ||||||  | |         ||  |||    |        ||    | |  |||      || ||  |      |||                           
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaa-gtccatttgattgattttagagaaaaagagaatcaatctgaggcttttg--tttgtttgttgcgagcag---------------------------

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|162183634|gb|FC359888.1|FC359888
EST:     AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAG                         GCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
genomic: AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctg ... atcttggcagGCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
EST: gi|67695047|gb|BJ955280.1|BJ955280
EST:     AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAG                         GCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
genomic: AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctg ... atcttggcagGCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
EST: gi|162157819|gb|FC334090.1|FC334090
EST:     AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAG                         GCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
genomic: AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctg ... atcttggcagGCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
EST: gi|162189554|gb|FC365776.1|FC365776
EST:     AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAG                         GCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
genomic: AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctg ... atcttggcagGCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGAC
EST: gi|67571682|gb|BJ944506.1|BJ944506
EST:     AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAG                         GCAATGTCGAAACCAGCTGCTTGGCATAGA
genomic: AATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctg ... atcttggcagGCAATGTCGAAACCAGCTGCTTGGCATAGA

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: 28

GAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctg ... atcttggcagGCAATGTCGAAACCAGCTGCTTGGCATAGATTTGGGTCGCAGAACCCAGACGATAGTGATGACGATAGCTCGCACTTCATAAGTGCAGTGTGTTGGAAGA




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