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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgcgctctcatttgatatcgttatattgatatctgttgtagcatttcttccgtctgttcgtttggactttttttacggctgttttgttctctt...

Basic information

species Physcomitrella patens
transcript PP1S28_399V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_399V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G108285_T01 (Zea mays), 5'ss of exon 2
GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgcgctctcatttg---atatcgttatattgatatctgttgtagcatttcttccgtctgttcgtttggactttttttacggctgttttgttctctt--
 || ||  ||||||| ||| | |||||||||||||||||||| || |||||||||||| || |     |||  | ||   || |  |||  ||     |  |  ||   ||  ||      ||| ||       |  || |    |  |||||  | ||  
ATGCATTTTGGTGGACGAGCAGGACAATGTTGTTGGCCATGAGTCAAAGTACAACTgtaagattctattctgctctgcttatctacttaatttctgcaccctattaatgttgtttgaactggtttgtggaacagtacttgatttgttatttgtcatgttag

upper sequence: PP1S28_399V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ31498 (Selaginella moellendorffii), 5'ss of exon 2
GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgcgctctcatttgatatcgttatattgatatctgttgtagcatttcttccgtctgttcgtttggactttttttacggctgttttgttctctt
|||||| |||||||| ||||| |||||||| || ||||||||||||||||| |||||| ||        |  |    | |       | |  | | | ||    | | |  | |||                                        
GTGTATCCTGGTGGACGAGAAGGACAATGTCGTCGGCCATGACTCCAAGTATAACTgtaagagaatagccagaaaaaaaaaaccggaagtcgtgtttttttcttcttcttcttcgtgaag------------------------------------

upper sequence: PP1S28_399V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ38651 (Selaginella moellendorffii), 5'ss of exon 2
GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgcgctctcatttgatatcgttatattgatatctgttgtagcatttcttccgtctgttcgtttggactttttttacggctgttttgttctctt
|||||| |||||||| ||||| ||||| || || ||||||||||||||||| |||||| ||        |  |    | |   |   | |  | | | ||    | | |  | |||                                        
GTGTATCCTGGTGGACGAGAAGGACAACGTCGTCGGCCATGACTCCAAGTATAACTgtaagagaatagccagaaaaaaaaaactggaagtcgtgtttttttcttcttcttcttcgtgaag------------------------------------

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|100367664|gb|BY984756.1|BY984756
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100448697|gb|CJ972996.1|CJ972996
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100399390|gb|BY954346.1|BY954346
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|162217577|gb|FC393981.1|FC393981
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208353466|gb|DC938701.1|DC938701
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208397465|gb|DC908299.1|DC908299
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAANGANAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208367267|gb|DC939825.1|DC939825
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100451948|gb|CJ975023.1|CJ975023
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAGTGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208390214|gb|DC941993.1|DC941993
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208386359|gb|DC932855.1|DC932855
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208358240|gb|DC930681.1|DC930681
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|19784534|gb|BQ040190.1|BQ040190
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100434315|gb|BY979047.1|BY979047
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208377735|gb|DC940847.1|DC940847
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|18363121|gb|BJ195193.1|BJ195193
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|18329541|gb|BJ161547.1|BJ161547
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208374313|gb|DC940670.1|DC940670
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|18331218|gb|BJ163227.1|BJ163227
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100365672|gb|BY948358.1|BY948358
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100368808|gb|BY984900.1|BY984900
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100424955|gb|BY976899.1|BY976899
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208357909|gb|DC934828.1|DC934828
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208376707|gb|DC902916.1|DC902916
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|162215822|gb|FC390887.1|FC390887
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208345096|gb|DC909458.1|DC909458
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208375497|gb|DC937012.1|DC937012
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|208389975|gb|DC938030.1|DC938030
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|67703862|gb|BJ964095.1|BJ964095
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|162192625|gb|FC370672.1|FC370672
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100388888|gb|BY988764.1|BY988764
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
EST: gi|100420599|gb|BY976088.1|BY976088
EST:     ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT                         GTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA
genomic: ACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCA

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: 32 (upstream exon), 32 (downstream exon)
Score: 13

GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgc ... atgtatccagGTCATTTAATGGAAAAGATAGAGAAGGAGAACTTGCTGCACCGTGCGTTCAGTGTCTTTCTTTTCAATTCCAAGCATGAGCTCCTGTTGCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACTgtgagttcgcgctctcatttgatatcgttatattgatatctgttgtagcatttcttccgtctgttcgtttggactttttttacggctgttttgttctctt

- - - - TGGTGG
- - - -  GGTGGA