Skip to another splice site:
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 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

...gatggggtttactttataatggacaggattgtagttttcgatgcgtgaacgtttacagatacgacatctcacctgattatatctgtcgaattttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATTTACTCCGTTGGACCCCACTTCAAGGAAGCCAACAGTTTCTTGTTGCCAT

Basic information

species Physcomitrella patens
transcript PP1S11_173V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S11_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 5
gatggggtttactttataatggacaggattgtagttttcgatgcgtgaacgtttacagatacgacatctcac-ctgattatatct-gtcgaattttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATTTACTCCGTTGGACCCCACTTCAAGGAAGCCAACAGTTTCTTGTTGCCAT
                                          |   || | ||| |    | ||| |||    || ||  | |||  |    | |||   ||   || ||  |||  || ||||| ||||| ||||||||| |||||||||| ||| | ||||| || ||||||||||| || || |  ||||||| ||| |
------------------------------------------gtacgatccttttctacgatgacttctagttctcatcgtttcttatttgttctttctcagAGCCTGGGGAAGTATGGAATCATCTGTATCGAGGATCTCATCCACGAGATCTACACGGTTGGGCCACACTTCAAGGAGGCGAATAACTTCTTGTGGCCTT
















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|7147844|gb|AW509766.1|AW509766
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|208365775|gb|DC951038.1|DC951038
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162206553|gb|FC382922.1|FC382922
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|37821482|gb|BJ579548.1|BJ579548
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|67694029|gb|BJ954262.1|BJ954262
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162227524|gb|FC403466.1|FC403466
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162209025|gb|FC385577.1|FC385577
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162275286|gb|FC451262.1|FC451262
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|37834457|gb|BJ592469.1|BJ592469
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162230791|gb|FC406422.1|FC406422
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTC
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTC
EST: gi|37840975|gb|BJ598983.1|BJ598983
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162209026|gb|FC385578.1|FC385578
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|67700234|gb|BJ960467.1|BJ960467
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162230790|gb|FC406421.1|FC406421
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162227523|gb|FC403465.1|FC403465
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162259014|gb|FC435125.1|FC435125
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|162259015|gb|FC435126.1|FC435126
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
EST: gi|208391789|gb|DC937979.1|DC937979
EST:     ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAG                         GCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT
genomic: ATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATT

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), 34 (downstream exon)
Score: 25

CCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAAAAGgtattgttat ... ttttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATTTACTCCGTTGGACCCCACTTCAAGGAAGCCAACAGTTTCTTGTTGCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacgtttacagatacgacatctcacctgattatatctgtcgaattttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATTTACTCCGTTGGACCCCACTTCAAGGAAGCCAACAGTTTCTTGTTGCCAT
                                             ttttttgt  CT-rich tract
                                           aattttttgta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggggtttactttataatggacaggattgtagttttcgatgcgtgaacgtttacagatacgacatctcacctgattatatctgtcgaattttttgtagGCACTTGGACAGTTCGGTATCATTTGTATTGAGGATCTCGTCCACGAGATTTACTCCGTTGGACCCCACTTCAAGGAAGCCAACAGTTTCTTGTTGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA