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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcctactctgctttttccaagtttcatttttcttgttcgagtttgtatggttagtctttggaatgggaaagtgtggaagcttgcttggtatttctgctgccgaccatctctcacgtcattacgcgtttacag

Basic information

species Physcomitrella patens
transcript PP1S6_173V6.1
intron # 4
splice site 5'
intron type U2

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|208374177|gb|DC945223.1|DC945223
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|100407592|gb|BY991770.1|BY991770
EST:     GGATTATCCGATTTTAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|67718087|gb|BJ968346.1|BJ968346
EST:     GGATCATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGG
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGG
EST: gi|67726582|gb|BJ976841.1|BJ976841
EST:     GGATCATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208346475|gb|DC917428.1|DC917428
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208395942|gb|DC915702.1|DC915702
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208370208|gb|DC952030.1|DC952030
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|67696865|gb|BJ957098.1|BJ957098
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|67725755|gb|BJ976014.1|BJ976014
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|162232709|gb|FC408116.1|FC408116
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|37824112|gb|BJ582178.1|BJ582178
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|100438460|gb|BY979968.1|BY979968
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGT
EST: gi|208393913|gb|DC946123.1|DC946123
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208359104|gb|DC930436.1|DC930436
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGA
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGA
EST: gi|208393221|gb|DC908044.1|DC908044
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCANTTGGATT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATT
EST: gi|208399428|gb|DC924858.1|DC924858
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|162232708|gb|FC408115.1|FC408115
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|37826519|gb|BJ584531.1|BJ584531
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208349443|gb|DC921931.1|DC921931
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208373323|gb|DC944966.1|DC944966
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|37846680|gb|BJ604688.1|BJ604688
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|67718044|gb|BJ968303.1|BJ968303
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGAC
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGAC
EST: gi|37826548|gb|BJ584560.1|BJ584560
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|37850883|gb|BJ608891.1|BJ608891
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|100378105|gb|BY949683.1|BY949683
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTG-CAATGATCGGGGATCAGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGT
EST: gi|67726544|gb|BJ976803.1|BJ976803
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208397369|gb|DC916323.1|DC916323
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|100400372|gb|BY954444.1|BY954444
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
EST: gi|208382280|gb|DC919268.1|DC919268
EST:     GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG                         GTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT
genomic: GGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGT

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: 34 (upstream exon), 22 (downstream exon)
Score: 6

GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcct ... gcgtttacagGTGTTGGCAATGATCGGGGATCAGTTGGATTTCGGCGACAGTGTCTGTGGTGCTGTTTTGAGCATTCGTTTTGGGGAGGACATCCTTAGCATATGGAACC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTGgtaaattcctactctgctttttccaagtttcatttttcttgttcgagtttgtatggttagtctttggaatgggaaagtgtggaagcttgcttggtatttctgctgccgaccatctctcacgtcattacgcgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA