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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatttttgttgaggctgcccatttctaagtttttaatgatgtagctgatgatatacgctaattctcttttagcgtatatcatcagctatcactc...

Basic information

species Physcomitrella patens
transcript PP1S197_115V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 9
TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatttttgttgaggctgcccatttctaagtttttaatgatgtagctgatgatatacgctaattctcttttagcgtatatcatcagctatcactc---
| ||||||||||| ||||||||||| || ||| ||||||| ||||| |||||||| || ||  | || ||| | || |||||||||||| |   ||| |||        |  || | |    | |  | ||||  |  | |   | |  ||  |  | | ||     |  || |    | | | ||   
TTAAAACAAACGATATGATGTTGGTCATATACTTGTCTTCTCTTATCCGGAGTGTCATCGCACTCCATAACTTGATCAATAACAAGgtaaattgtttctgt--------cttatctattgaatatagaagatgcgggagttaggagatacttgtcatttattgtaagacttccttttatttgattccag

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G061745_T02 (Zea mays), 5'ss of exon 8
TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtata---agattt-ttgttgaggctgcc-----catttctaagtttttaatgatgtagctgatgatata-cgctaat--tctcttttagcgtatatcatcagctatcactc---------------------------------------
|||||||||||||||||||||||||||| ||||||||||| || || ||||| || |||||  | |||||  | || || || |||||  |   | || | ||  |||  |||       ||| | |   ||  |  |      | ||||    ||  |  | |  || ||| ||  | | |||      | |  ||                                        
TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcatatctgtttctgatactgtttcagtcatgtatgcattccttgtagataggttgataccttagtgacattgatcacttgtaatgga-atcgctcaattttgctgtggacatgaaatcttgtctgttaattgctgtgattccag

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 8
--------------TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatttttgt-tgaggctgcccatttctaagtttttaatgatgtagctgatgatatacgctaattctcttttagcgtatatcatcagct-----atcactc-------------------------------------------------
              ||||||||||||||||||||||||| || || |||||||| || || |||||||| |||||  | |||||  | || || || |||||      ||||| | ||   |||    | | | |||   |  || || | |   || || |   | ||    || |  | |  | ||  ||       |||||||                                                 
TTTCTTTTGTACAGTGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtttttatctgcttctggtgctgtttcagtccct--tggtgcatcccttg-tagattttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccag

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G368908_T03 (Zea mays), 5'ss of exon 6
TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatttttgt-tgaggctgcccatttctaagtttttaatgatgtagctgatgatatacgctaattctcttttagcgtatatcatcagctat-----cactc-------------------------------------------------
||||||||||||||||||||||||| || || |||||||| || || |||||||| |||||  | |||||  | || || || |||||      ||||| | ||   |||    | | | |||   |  || || | |   || || |   | ||    || |  | |  | ||  ||  ||     |||||                                                 
TGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtttttatctgcttctggtgctgtttcagtccct--tggtgcatcccttg-tagattttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccag

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgta-taagatttttgttgaggctgcccatttctaagtttttaatgatgtagctgatgatatacgctaattctcttttagc-gtatatca--tcagctatcactc
|||||||||| || ||||||||||| ||||| || || || || || || |||||||| ||| | |||||| | || |||||||||||| || |   | |  | |        | || |   ||  |  | |  |||    ||   |  | ||  |   ||| ||| | ||||    |    | | ||  
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagtttt---ttcatgctaac-tagacattggccttggttacctgattttaagctggatattgagttgaatgttacga

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|208351962|gb|DC925771.1|DC925771
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
EST: gi|7693546|gb|AW761652.1|AW761652
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
EST: gi|208368978|gb|DC955063.1|DC955063
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
EST: gi|162212342|gb|FC388070.1|FC388070
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
EST: gi|7648296|gb|AW739279.1|AW739279
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATC
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATC
EST: gi|162169877|gb|FC346233.1|FC346233
EST:     CTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
EST: gi|208371459|gb|DC955795.1|DC955795
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
EST: gi|37826136|gb|BJ584148.1|BJ584148
EST:     CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG                         ATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT
genomic: CTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTT

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: 28 (upstream exon), 16 (downstream exon)
Score: 2

TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtataagatt ... tcgcttgcagATTTTGAATAAGGAGCACGAGAGAATTGCAGATGCGGCATCGGCTAGTGTTTCTGCTATCACAGTTTAGGTAGTGTAACACCGGTGCTCGGCTCTCGAGT




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