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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG

Basic information

species Physcomitrella patens
transcript PP1S31_254V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
        ||| ||||    |   || |      | |   | ||     | |     | |||   | | |   || |    | ||  | ||   | |||||| ||||  || || || ||||||||||| ||||| |||||||| ||||| || || ||||| || ||||| || || |||||||| || ||||| ||||
--------gtatgcaaccatg---tttgagaatcaaaacatattagaaatgttcatttagattgtaacattc-tcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
---------------------aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
                      ||  ||  | | |  |    | || | || | |||  ||   |  |  ||      |   || |||  | | || ||     |  |||    |   |||||||| || |||||||| ||||| |||||||| || |||| ||| |||||||| ||  | || || ||||||||||| || ||||| ||||| || ||||
gttgagtgttaaccacttcctcatgcttccttctcctttttcagttccattgc-tatcatccaatggtaatacatatatgtttgacatatt-tatcttc----ttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G12710.1 (Glycine max), 3'ss of exon 3
-----------aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagt--tcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
            || | || |    | | | |  ||   | || |  |   | |||||||        |  |     |    |   || ||   | ||  | |        |||||| ||||||||| || ||||||||||| ||||| || ||||| |||||||| ||  | || |||||| |||||||  | ||||| ||  | || ||||
gtatgttctttgatctcttctgaagagtcgtg--ttatatctcttgcatcattttccttggggtcatatcaagaaattaacttactcttaatttttgtcatttccaaatctagGATTTCACAGCTAAACTCTCTGATTTTGGGCTAGCTAAGGATGGCCCTGAAGGGGAAGACACACACGTAACAACACGCATAATGGGAACACAAGGTTATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G33470.1 (Glycine max), 3'ss of exon 3
-----------aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttc---ttgggtgtc-agGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
            || |||| |    |||   |       | | | ||  |||      ||       |  ||  | | | |    |||  ||  |   ||   |||    || |||||| |||||||||||| || |||||||| ||||| || ||||| |||||||| ||  | || || ||| |||||||  | ||||| ||  | || ||||
gtatgctctctgatcttttctgaagaatcatgttacatctcttgcatcatcttcctagtgaccatatcaagaaattaacttggacccttcaatttttatctctttgaaaatctagGATTTCACAGCTAAGCTCTCAGATTTTGGGCTAGCTAAGGATGGCCCTGAAGGGGAAGACACACATGTAACAACACGCATAATGGGAACACAAGGTTATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
-aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
  || |    ||  ||  | | |  ||  ||   |||  | | | | |  |     || | |   |||           |||| || || ||     | |||| ||||  || || || ||||||||||| || || |||||||| |||||||| || || || ||| |||||||| | |||||||| || ||||| ||||
gtatgtgagttaaccaggaaaaaggttt-ttaattattttttatccatcctcca--acataaaaacataa---------aaacataattgttt----ttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 4
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
        ||| |  |   | | |   | || | | |   |  ||||    |    | |  | | ||  ||  |     || || ||||||      ||||| ||||  |||||||| ||||| ||||| || || ||||| || || |||||||| || || || ||||| || ||||| |||||||||||||||||||
--------gtaggtgacttaaaat---gctttgcaaatagtagtcctaacttat--ccttgtcttatt-tcaatttgtgaaacttgttctt-----ccagGACTACAATGCTAAGCTTTCTGACTTTGGACTTGCCAAAGACGGTCCAGAAGGAGATAAGACACATGTATCTACTCGTGTAATGGGCACCTATGGCTATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv04s0008g02070.t01 (Vitis vinifera), 3'ss of exon 3
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
                  |  |  |      ||  |  ||| | | ||||      ||| |      | ||    || |  | |  |||||   |  ||||||||||| ||||| || |||||||| || |||||||| || || || ||||| ||| | |||||||||||||| ||  | ||||||||  |||||||||
------------------gtaagctcttccccgcctgctctctccattgtcaatctcttcaaaatggc-tcaaagcttactcttctttcttcttt-ccagGATTACACTGCTAAACTCTCTGATTTCGGGCTAGCGAAGGACGGTCCAGAAGGCGACGAGACTCACGTATCAACCCGAATAATGGGCACACATGGCTATG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ19239 (Selaginella moellendorffii), 3'ss of exon 4
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
            | | ||||   |   |    | | |  |  |        |||    | |      | |   || | ||| |           | |||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||||||||| || || || || |||||  ||||||| || || ||||| |
----------gtg-agtagaagataaagaaatgaagaaacaatct------tggagactaacaaacccgtgactcgttaaatcc----------tctcagGACTACACGGCCAAGCTCTCGGATTTCGGCCTCGCGAAAGATGGCCCGGAAGGAGACAAGACGCATGTTTCCACACGAATCATGGGAACTTACGGCTACG

upper sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ22709 (Selaginella moellendorffii), 3'ss of exon 4
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
            | | ||||   |   ||   | | |  |  |        |||    | |      | |   || | ||| |           | |||||| ||||| || ||||| || ||||| ||||| ||||||||||| || ||||||||||| || || || || |||||  ||||||| || || ||||| |
----------gtg-agtagaagataaagtaatgaagaaacaatct------tggagactaacaaacccgtgactcgttaaatcc----------tctcagGACTACACGGCCAAGCTCTCGGATTTCGGCCTCGCGAAAGATGGCCCGGAAGGAGACAAGACGCATGTTTCCACACGAATCATGGGAACTTACGGCTACG

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: 28 (upstream exon), 35 (downstream exon)
Score: 7

GATAGCATTAGGAGCTGCAAGTGGATTGGCATTCCTCCATGAAGCAGTGAAACCAGTTATCTATCGTGATTTCAAGACGTCCAACATATTATTGGATAGTgtgagtcatc ... tgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG
          acttgat  putative branch site (score: 7)
                                         ttctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA