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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattagctagttgaattgactatggcgctgaactcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG

Basic information

species Physcomitrella patens
transcript PP1S276_75V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 3
---------gt-tagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcg---aactcaagtaatgcacttgcttatgatgggat-------tagct--agtt--gaattgactatggcgc---tgaac--tcaatgt-----agGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
         || ||||    | | |   | | |  |   | |  | |     || ||     |  ||  | ||   | ||  ||    |      |  ||    |    || |||||||||  ||       |||||  | ||  || ||  ||          |||||  |     |     |||| ||||| || ||||| || || |||||||||||||| || ||  |||||||| | |||||||| || ||||||||||||||||| || || || ||||
gtatgccacgtatagtaaactgttcgtgttcttatgatgcaa--tcctatcattgcttaaattcagagttttctgaaaaatgactgaacatttggcataaactgtttgttttcttatgatgcaatcctatcatagcttaaattcagagttttctgaaaaatgagtgaacatttggcatgcaccagGTTGAGCTGGAGGACCCTGTTGAAAATATTGGAGCCAAATTAGTCCGGCAAGCTGCAGCCAAGACAAATGATTTGGCTGGTGATGGGACAACGACTTCTG

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 3
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttgga--aatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattagctagttgaattgactatggcgctgaactcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                                            | | ||  ||| |  | ||  |||       | |||   |     ||||   | || |  |  ||  ||  ||    || || | || ||  | ||| |||    | |||| || || || || || || || ||||||||||| |||||||||||||||||  | || |||||||| ||||| ||||| ||||| || || || ||||
--------------------------------------------ttttcttattgaacaagtcaactggaggtttc-tggattatctgtgtaacctagttcc--agaatttgagcagaattttcaagtaacgat--ctctgtact----gcagGTTGAACTGGAGGATCCTGTTGAAAATATTGGAGCTAAGTTGGTTAGGCAAGCAGCAGCAAAGACCAATGATTTAGCTGGAGATGGCACAACTACTTCTG

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 3
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattagctagttgaattgactatggcgctgaactcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                                        | | | | ||   || |    |   |   | || |    | | |   ||| |  |   |  |||| ||   |||| || |  |||||   ||  | |||  ||    |||||| ||||| || ||||| || || || |||||||| || ||||| ||||||||| | || |||||||||||| | ||||| ||||| || ||||||||||
---------------------------------------ctctctgttctttctgaaggcttataggttatcatgcaa-gtagtagcgtagttaa---gtatatgttgaatttaggtaat--aattgctaat--ccctgttct----gtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAAGCTGCAGCTAAGACCAACGATCTTGCTGGAGATGGGACAACCACCTCTG

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 2
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattagctagttgaattgactatggcgctgaactcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                                  ||    | | | | |         || || |  |||    ||       | ||||       ||| || || | | |||     |||   |||| | |||    | |        |||| ||| | || || || || ||||||||||| ||||||||||| || |||||  |||||||||| ||||| |||||||||||||| ||||| ||||| |
----------------------------------tttgaatttgtttacgtggataggatttcatttgaattgtgt-------ttaagtggattgtttgtttgtgtttgtattgat--gttttgttgaatttggtttggta--------agGTTGAGTTGGAGGATCCCGTTGAGAATATTGGTGCCAAGTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGG

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 2
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattagctagttgaattgactatggcgctgaactcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                                                    || ||| |    |  |      |      | |  | |  ||     |    |  |  |  |   |  ||  ||    | | |   |  | |    | |||| ||| | || || || || ||||||||||| ||||||||||| || |||||  |||||||||| ||||| |||||||||||||| ||||| || || |
--------------------------------------------------tgtttgaatttgtttatgtggataggatttcatttgaattttgtttaagtgggttttttgggtgtttgttttgatgctttgttgaatttgatttgg-gaagGTTGAGTTGGAGGATCCGGTTGAGAATATTGGCGCCAAGTTGGTGAGACAAGCAGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACTTCGG

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattag--ctagttgaattga---ctatggcgctgaactcaa---tgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                                                                               | |   || || | | | | || || |||   || |  ||  || || |||    ||  |     ||||      ||||||| ||| | |||||||| || ||||| ||||| || ||| | || ||||||||  ||||||| ||||| || ||||||||||| ||||| || || ||||
-------------------------------------------------------------------------------gtatggaattattacccct-ctgataatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG

upper sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 3
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattagctagttgaattgactatggcgctgaactcaa-tgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                                                  |||   |  | ||||    ||   | |     ||| |||||   |  |    |  |     |  |  ||  | | | | |   |   ||   |||  | ||||| ||| | || || || || ||||||||||| || || || || || |||||  |||||||||||||||| |||||||| ||||| || || || ||||
-----------------------------------------------atgcctaccatctgtccttg--acgttgagattgtctccagtaa-atatctcaacacaaatttgtccgtgag--gcacttattgatgttttgttatcacctatagGTTGAGTTGGAGGATCCTGTTGAGAATATTGGTGCTAAATTAGTGAGACAAGCAGCTGCCAAGACCAACGACTTGGCTGGGGATGGGACAACAACATCTG

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|162163834|gb|FC340056.1|FC340056
EST:     AGTATGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|208357238|gb|DC910649.1|DC910649
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|162187015|gb|FC363421.1|FC363421
EST:     AGTATGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|18354362|gb|BJ186418.1|BJ186418
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGA
EST: gi|67572411|gb|BJ945235.1|BJ945235
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTG
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTG
EST: gi|67569513|gb|BJ942337.1|BJ942337
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|18369385|gb|BJ201471.1|BJ201471
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|56082257|gb|BJ176717.2|BJ176717
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|162186625|gb|FC363597.1|FC363597
EST:     AGTATGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|18372339|gb|BJ203941.1|BJ203941
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|18355098|gb|BJ187157.1|BJ187157
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGA
EST: gi|18372360|gb|BJ203962.1|BJ203962
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|100363541|gb|BY966441.1|BY966441
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|22492170|gb|BU052093.1|BU052093
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
EST: gi|18366797|gb|BJ198876.1|BJ198876
EST:     AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA
genomic: AGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAA

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: 19 (upstream exon), 34 (downstream exon)
Score: 7

AGTCGGTGTCACTTTGGGACCCAAGGGACGCAACGTCGTGCTTGAAAGTAAGTACGGGTCCCCCAAGATTGTGAACGACGGTGTCACCGTGGCCAAGGAGgttagtggtg ... ctcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttatgatgggattagctagttgaattgactatggcgctgaactcaatgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG
                          aattgac  putative branch site (score: 7)
                       ttgaatt  TA-rich tract