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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATCGAGAAACCCAATGAGATATTTGCGGACTGAAAAGCAGAAACTAACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttcccttgtctgatgatatatatatatatatatatatataattatgttatcgagattcgttatccttgccaatttatgctattgttcacctacctagctgcatgtaaaatgccactgcagtttgttcccaatttttctgttcatttcccatcgttgtttactgatcgggggttgtttgaattctgcag

Basic information

species Physcomitrella patens
transcript PP1S395_19V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S395_19V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA16G25750.1 (Glycine max), 5'ss of exon 10
GAAAATCGAGAAACCCAATGAGATATTTGCGGACTGAAAAGCAGAAACTAACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttcccttgtctgatgatatatatatatatatatatatataattatgttatcgagattcgttatccttgccaatttatgctattgttcacctacctagctgcatgtaaaatgccactgcagtttgttcccaatttttctgttcatttcccatcgttgtttactgatcgggggttgtttgaattctgcag
 |  | |  || |||   | | | || ||   |||||       |  ||    |||| |||||| || || |||||||||||| ||||||| |||||||||||   ||| |   |||||   || ||| |  ||| || ||||   ||    ||| || ||||  |     |   |||| | | | || |   | ||                                                                                                
TAGGAGCAGGATACCAGCTCATAGATATGATAACTGAGCCTTTTAGGCTGGTCCGTCGTTGTGAAGTGACAGCCATACTTGTTTTGTATGGCCTTCCTAGgta---tcctt---ctgataccatctattttcata-atctatagtgtttgcatatgga-attcaatggatat---aattcaagattttatattcatag-----------------------------------------------------------------------------------------------

upper sequence: PP1S395_19V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA02G06720.1 (Glycine max), 5'ss of exon 9
GAAAATCGAGAAACCCAATGAGATATTTGCGGACTGAAAAGCAGAAACTAACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttcccttgtctgatgatatatatatatatatatatatataattatgttat-cgagattcgttatccttgccaatttatgctattgttcacctacctagctgcatgtaaaatgccactgcagtttgttcccaatttttctgttcatttcccatcgttgtttactgatcgggggttgtttgaattctgcag
 |  | |  || |||   | | | || ||   || ||       |  ||    |||| |||||| || || |||||||||||| ||||||| |||||||||||   ||| |   |||||    | ||| |  | |   || |||| || |   ||  |  ||||  | |  |    |||| | |  ||| |  |   |  |||                                                                                           
TAGGAGCAGGATACCAGCTCATAGATATGATAACCGAGCCTTTTAGGCTGGTCCGTCGTTGTGAAGTGACAGCCATACTTGTTTTGTATGGCCTTCCTAGgta---tcctt---ctgatatcgtctattttcaaa---atctatagtttttgcatatggaattcactctaata--taattcaagg-attttatattga--tag-------------------------------------------------------------------------------------------

upper sequence: PP1S395_19V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA01G38640.3 (Glycine max), 5'ss of exon 7
GAAAATCGAGAAACCCAATGAGATATTTGCGGACTGAAAAGCAGAAACTAACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttcccttgtctgatgatatatatatatatatatatatataattatgttatcgagattcgttatccttgccaatttatgctattgttcacctacctagctgcatgtaaaatgccactgcagtttgttcccaatttttctgttcatttcccatcgttgtttactgatcgggggttgtttgaattctgcag
    | |  |  ||| |   | | |  ||   ||||||    | |   | |  ||||||||||| || || ||||| |||||| ||||||| |||||||||||     |||| |   |  || ||  |  ||| || || |  |  ||   |    || ||||   ||   |   |||| |   | ||  | |  ||  |||                                                                                           
TTGGAGCAGGCTACCGAGCCATAGACATGATAACTGAACCTTATAGGTTGATCCGTCATTGTGAAGTGACAGCCATTCTTGTTTTGTATGGCCTTCCTAGgta----tccttcttatacaatctactttcata-atctaca-gtgcttgcata--tgacattccccatatat---aattcaatttctt--ttatgtatatag-------------------------------------------------------------------------------------------

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|37853216|gb|BJ611224.1|BJ611224
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
EST: gi|162191986|gb|FC367199.1|FC367199
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
EST: gi|162268651|gb|FC445148.1|FC445148
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
EST: gi|37822207|gb|BJ580273.1|BJ580273
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
EST: gi|162257370|gb|FC433453.1|FC433453
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
EST: gi|162268650|gb|FC445147.1|FC445147
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
EST: gi|100445528|gb|CJ975677.1|CJ975677
EST:     ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAG                         ACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG
genomic: ACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCG

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: 23 (upstream exon), 32 (downstream exon)
Score: 4

GAAAATCGAGAAACCCAATGAGATATTTGCGGACTGAAAAGCAGAAACTAACTCGTCATTGTGAGGTCACTGCCATACTTGTTCTGTATGGACTTCCTAGgtaagttccc ... aattctgcagACTGCTCACAGGGTCTATCTTGGCTCACGAACTTATGCATGCTTGGATTCGTCTGCAAG




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