Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGTCAGTCGACCAAAGTTCCCGAGGACCCAGAGATCAAAGCTTGGTTGGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggactaccttaagcatccctgcaatttttgttgtgtaagaattctttgttcagtgctattctatcgtatggtttgccagatcgccttccatatcaaatttggagagcgttcaaaatttgctcgaagatgtggttagtcattgtcgaacataataatgtcgtactgagtgtggactattgtggcag

Basic information

species Physcomitrella patens
transcript PP1S264_34V6.1
intron # 8
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|208386880|gb|DC956891.1|DC956891
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|67726166|gb|BJ976425.1|BJ976425
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|37836413|gb|BJ594421.1|BJ594421
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|67720297|gb|BJ970556.1|BJ970556
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|37825230|gb|BJ583296.1|BJ583296
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|18339223|gb|BJ171250.1|BJ171250
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|37827952|gb|BJ585964.1|BJ585964
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|15730234|gb|BI741746.1|BI741746
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|67693669|gb|BJ953902.1|BJ953902
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162162327|gb|FC338304.1|FC338304
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTTTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162206837|gb|FC382699.1|FC382699
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTTTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162241037|gb|FC416668.1|FC416668
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGANACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162200495|gb|FC376156.1|FC376156
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162180761|gb|FC357846.1|FC357846
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162235225|gb|FC411282.1|FC411282
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162236927|gb|FC412878.1|FC412878
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162158379|gb|FC334174.1|FC334174
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|67725401|gb|BJ975660.1|BJ975660
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162180762|gb|FC357847.1|FC357847
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGANACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|67697855|gb|BJ958088.1|BJ958088
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|7047301|gb|AW477195.1|AW477195
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|37820987|gb|BJ579053.1|BJ579053
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|18335638|gb|BJ167658.1|BJ167658
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
EST: gi|162206838|gb|FC382700.1|FC382700
EST:     GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAG                         GTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT
genomic: GGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGT

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: 31 (upstream exon), 32 (downstream exon)
Score: 19

GAATGTCAGTCGACCAAAGTTCCCGAGGACCCAGAGATCAAAGCTTGGTTGGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggacta ... attgtggcagGTAAGAAAGGCGACGCCATGATTGAGGACTCGTCTGAAACAGCCGCAGAGTCAGCCACAGGAACTACTGATACAATGGACACTTCAGCCTAGACTTCACA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGTCAGTCGACCAAAGTTCCCGAGGACCCAGAGATCAAAGCTTGGTTGGCTTTGGGTACTAAGTCCAAAAAGAAGGGTGGTGGTAAGAAGAAAAAAGgtgaggactaccttaagcatccctgcaatttttgttgtgtaagaattctttgttcagtgctattctatcgtatggtttgccagatcgccttccatatcaaatttggagagcgttcaaaatttgctcgaagatgtggttagtcattgtcgaacataataatgtcgtactgagtgtggactattgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA