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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagcgtgcctactgcaccaaattatttcgtaccagaaaatgagttttggtgatcgttttacagttcaaaaaactgttggtaatagtactgaagctaatcctacatggcgatcaactgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCATATGCCAAAGGAGCTACCGGAAATGTGGCCACCGAGGATGTGATCTACT

Basic information

species Physcomitrella patens
transcript PP1S138_43V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S138_43V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G26800.2 (Arabidopsis thaliana), 3'ss of exon 8
gtatgaagcgtgcctactgcaccaaattatttcgtaccagaaaatgagttttggtgatcgttttacagttcaaaaaactgttggtaatagtactgaagcta--atcctacatggcgatcaactgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCATATGCCAAAGGAGCTACCGGAAATGTGGCCACCGAGGATGTGATCTACT
                                                  |  || |     | | ||   || |     ||   ||||  |||  |  ||   |   |||||    |      ||  |||||||| || ||  | || ||||||||  | || ||  | ||||| ||||||||||| ||||||||| | |||||||| ||||| || |||||| | ||| 
-------------------------------------------------gtaagtcaagcactaatagaagaatatttgattataaatataacttcatttatggtttgacatg-tattggtgcaaaaacagATGGGAATAAGCATAGTAGACTCATCAATTGCCGGATTAGGCGGCTGCCCATATGCAAAAGGAGCTTCAGGAAATGTAGCCACAGAAGATGTGGTTTACA

upper sequence: PP1S138_43V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 7
gtatgaagcgtgcctactgcaccaaattatttcgtaccagaaaatgagttttggtgatcgttt-tacagttcaaaaaactgttggtaatagtactgaagctaatcctacatggcgatcaactgaat----------gcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCATATGCCAAAGGAGCTACCGGAAATGTGGCCACCGAGGATGTGATCTACT
                                        ||   || |||     | | | | |  |    | |||  |  | | |    || |    ||      |  |     ||   || ||           |||||||| || ||     | || || || || || || || || ||||||||||||||||| |||||| | || || |||||||||||||||||  | ||| 
----------------------------------------aagtagaatttcaaacaccatatatgtaaccaagaaatgtaattgcagatatattaggcctttcttcatttcattgtcctttggattttttggtccacagATGGGGATTAGCACCATAGATTCCTCTGTTGCTGGTCTTGGAGGATGCCCATATGCCAAGGGAGCTTCAGGGAACGTGGCCACCGAGGATGTTGTTTACA
















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|208362066|gb|DC950501.1|DC950501
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|208358876|gb|DC957648.1|DC957648
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|162189221|gb|FC366730.1|FC366730
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37822313|gb|BJ580379.1|BJ580379
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|208400825|gb|DC925105.1|DC925105
EST:     TCCACGACACTTACGGGCAGGCTNTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|208361217|gb|DC957686.1|DC957686
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37839517|gb|BJ597525.1|BJ597525
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37850965|gb|BJ608973.1|BJ608973
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|208355106|gb|DC922208.1|DC922208
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|162189220|gb|FC366729.1|FC366729
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37852376|gb|BJ610384.1|BJ610384
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37828735|gb|BJ586747.1|BJ586747
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|208392263|gb|DC949625.1|DC949625
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37850294|gb|BJ608302.1|BJ608302
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|162158069|gb|FC334977.1|FC334977
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|162207541|gb|FC383994.1|FC383994
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37826207|gb|BJ584219.1|BJ584219
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|162218483|gb|FC395060.1|FC395060
EST:     TCCACGACACTTACAGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAATGTGGTGGACTCATCGGTGGCGGGACTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|37826615|gb|BJ584627.1|BJ584627
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|162158070|gb|FC334978.1|FC334978
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
EST: gi|208379917|gb|DC927643.1|DC927643
EST:     TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAG                         ATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA
genomic: TCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCA

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: 26 (upstream exon), 31 (downstream exon)
Score: 3

GCTTGAAGCTGTGATGGCTGTGGTGCCAGTCGAGAGCCTGGCGGTGCATTTCCACGACACTTACGGGCAGGCTCTGGTAAACATCCTCGTCGCACTTCAGgtatgaagcg ... ctgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCATATGCCAAAGGAGCTACCGGAAATGTGGCCACCGAGGATGTGATCTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgttggtaatagtactgaagctaatcctacatggcgatcaactgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCATATGCCAAAGGAGCTACCGGAAATGTGGCCACCGAGGATGTGATCTACT
                      agctaat  putative branch site (score: 3)
          taatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaagcgtgcctactgcaccaaattatttcgtaccagaaaatgagttttggtgatcgttttacagttcaaaaaactgttggtaatagtactgaagctaatcctacatggcgatcaactgaatgcagATGGGCATCAGTGTGGTGGACTCATCGGTGGCGGGCCTGGGCGGATGCCCATATGCCAAAGGAGCTACCGGAAATGTGGCCACCGAGGATGTGATCTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG