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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCAGGACAGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaagtcatatttttttctgacctccttgtacgagatgtgtaagtaatcttcatgtgtttttgttgttcttgaagagctagtcaatctcccataggttgt...

Basic information

species Physcomitrella patens
transcript PP1S70_132V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_132V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT1G65590.1 (Arabidopsis thaliana), 5'ss of exon 9
ATTTCAGGACAGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaa--gtcatatttttttctgacctccttgtacgagatgtgtaagtaatcttcatgtgtttttgttgttc-ttgaagagctagtcaatctcccataggttgt
||||||| |   |||||   |||||||||| |||||||||||||||||||||  | ||| ||||   |||   | | || ||     | | ||    || | |  ||  |  |  ||  |   |||  ||| ||| ||                         
ATTTCAGCAAGATCTTTAAGTTTAAATTTGTCCACTTGGGTGGTGATGAAGTAAATACAAgtaatgatcaatatctcttttgtttatcatatatcctatctatg-gtgttggttttgattacatgtacttcgttgcag-------------------------
















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|100452525|gb|CJ975314.1|CJ975314
EST:     AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAG                         GTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
genomic: AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaagtcata ... atgtatctagGTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
EST: gi|100424280|gb|BY958405.1|BY958405
EST:     AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAG                         GTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
genomic: AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaagtcata ... atgtatctagGTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
EST: gi|162274270|gb|FC450238.1|FC450238
EST:     GGTGATGAAGTTGACACAG                         GTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
genomic: GGTGATGAAGTTGACACAGgtaagtcata ... atgtatctagGTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
EST: gi|22492472|gb|BU052395.1|BU052395
EST:     AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAG                         GTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
genomic: AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaagtcata ... atgtatctagGTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
EST: gi|208364361|gb|DC950662.1|DC950662
EST:     AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAG                         GTTGCTGGGAGCGAACTTCCCACATTCAGAACTG
genomic: AGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaagtcata ... atgtatctagGTTGCTGGGAGCGAACTTCCCACATTCAGAACTG

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: 14 (upstream exon), 22 (downstream exon)
Score: 1

ATTTCAGGACAGTCTTTCCATTTAAATTTGCCCACTTGGGTGGTGATGAAGTTGACACAGgtaagtcata ... atgtatctagGTTGCTGGGAGCGAACTTCCCACATTCAGAACTG




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