Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCCGATGCTGACCCCAAACCTACTCCCCCTGCTGACCACCTGCGCAAGGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcatttgaatgccctttctcacacttcgttttgggaattaggttagtgaaatctcctgcactgtttcttctgctctttttagtactctattactgacgatttcactgcgcgattttatcttcctcag

Basic information

species Physcomitrella patens
transcript PP1S424_33V6.1
intron # 1
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|162189630|gb|FC366268.1|FC366268
EST:     -GTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162205237|gb|FC380919.1|FC380919
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAA                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162173184|gb|FC348731.1|FC348731
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|208400375|gb|DC925013.1|DC925013
EST:     GGTTTT-TACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTTTAGGAA-GGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162163114|gb|FC340168.1|FC340168
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|7067017|gb|AW496872.1|AW496872
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162216168|gb|FC392585.1|FC392585
EST:     TACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: TACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162258043|gb|FC434137.1|FC434137
EST:     GG-TTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|67693097|gb|BJ953330.1|BJ953330
EST:     TTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: TTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162258044|gb|FC434138.1|FC434138
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|37852568|gb|BJ610576.1|BJ610576
EST:     GTTTTCTACAGGATGGACTTGAACGACCCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGG-TCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GTTTTCTACAGGATGGACTTGAACGA-CCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|37836693|gb|BJ594701.1|BJ594701
EST:     TATTGTCGCTCTTTCAG                         GTGCACATACTNTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: TATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162203752|gb|FC378627.1|FC378627
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162218122|gb|FC394972.1|FC394972
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162243487|gb|FC425183.1|FC425183
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|67698721|gb|BJ958954.1|BJ958954
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|22132379|gb|BQ827122.1|BQ827122
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGG
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGG
EST: gi|162201175|gb|FC377682.1|FC377682
EST:     ACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: ACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162160091|gb|FC335961.1|FC335961
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162205180|gb|FC381278.1|FC381278
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162229041|gb|FC404244.1|FC404244
EST:     GGTTTTCTACTGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162156803|gb|FC333615.1|FC333615
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|208395161|gb|DC915970.1|DC915970
EST:     TACAGGATGGACNTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: TACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162271054|gb|FC447121.1|FC447121
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162209028|gb|FC385580.1|FC385580
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|19786514|gb|BQ040490.1|BQ040490
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAA                         GTGCACATACTCTAGGAAAGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|162229686|gb|FC403996.1|FC403996
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
EST: gi|100366593|gb|BY985201.1|BY985201
EST:     GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAG                         GTGCACATACTCTAGG
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGG
EST: gi|208346717|gb|DC917500.1|DC917500
EST:     GGTTTT-TACAGGATGGAC-TGAACGACCAAGATATNGTCGCTCTCTCAG                         GTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA
genomic: GGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGA

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), 32 (downstream exon)
Score: 55

CTTCCCGATGCTGACCCCAAACCTACTCCCCCTGCTGACCACCTGCGCAAGGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcattt ... tcttcctcagGTGCACATACTCTAGGAAGGGTTCACCCAGAACGCAGTGGATTCGGGCAGAAAGAAACCAAGTACACTAAGAACGGGCCAGGCAAACCAGGAGGTTCCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCCGATGCTGACCCCAAACCTACTCCCCCTGCTGACCACCTGCGCAAGGTTTTCTACAGGATGGACTTGAACGACCAAGATATTGTCGCTCTCTCAGgtatgcatttgaatgccctttctcacacttcgttttgggaattaggttagtgaaatctcctgcactgtttcttctgctctttttagtactctattactgacgatttcactgcgcgattttatcttcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA