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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

Basic information

species Selaginella moellendorffii
transcript EFJ21839
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 5
--------------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                     | | |        |  |      || ||| || |    |   |   |||| |    |||    |||  ||| |      ||| |||||||||||||||||||||||||| || ||||||||||   |||| || || || ||  | ||||| |||||  |||| || ||||| ||  |||| 
gtgctgttgatcggttcacgatgaacgaagctgacagtgaacaatcgtgcctgaagttctgaaca--gttgacgaagtttaat-taactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 5
----------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttctcata-aactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                 ||      ||    |   |   |  |||     |  |  |    |  |||| |     |  | |   | |||| |   | |||||||||||||||||||||||||| ||| || |||||||||  | |||| ||  | || ||  | |||||  | ||  |||| || ||||| ||  ||   
cagttacatcgatcgtttacagcagcgtcaatactgtaataattgaccaaactgtcaaagcagtttgtgacaacattacgtgtgattttggtgcgcgcagGGAGATCATGCACGCGATGTGGAGGCCGCAGAAGTTCAAGGCGATCTACCTGATGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCGGCGGCGAGC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
--gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatg-----------ttgtcatcttttc----tcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
   |  ||    ||   |||  | |||  |   | |||  |||  ||              |  | |    ||     |       || |||     ||||||||||||||||||||||||||| ||    ||||||||||   |||| ||  | || ||  | ||||| |||||  |||| || ||||| ||  |||| 
gcatgtgccgaggccgttttgtccgttgatttgttgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G067022_T02 (Zea mays), 3'ss of exon 5
---gtaagctttcgcttctttcgctgttcttgca---tggatcgataggctatgttgtcatct---tttctca-taaactttgatcttcc-------cagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
   | | |  |   ||| |||   |   | |  |   |   ||  ||    || || |  | |   ||||||| | |  | ||||   ||       |||||||||||||||||||||||||||||| |  ||||||||||   |||| ||  | || ||  | ||||| |||||  |||| || ||||| ||  |||| 
cgtgaaggactctccttttttttatcagcatatactctatgtctctatctcattttctattttaaatttctcactgatttctgatgccccgcgcgcgcagGGAGATCATGCACGCGATGTGGAAGCCTCGCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTTCCGTCGGCGGCGGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------gtaagctttcgcttctttcgctgttc----ttgcatggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                                                 || |  ||| | |   |||   ||||     | | |   |   |      |||     | | |   || |      | |     ||||||||||||||||||||||||||| || || |||||||||    |||| || || || ||  | |||||  | ||  |||| || ||||||||| | || 
gtaagcctcagctgccagcagtctatatctatacccacacacagcagaagtgaagtttaggtcacttcagagttcagagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaaatgggccggttggtgcagGGAGATCATGCACGCGATGTGGAAACCGCACAAGTTCAAGCTCATCTACCTGGTGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCCGCCTCCGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G149481_T04 (Zea mays), 3'ss of exon 4
-------------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatc-ttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCAC-GGCA
                    |||      | |   |   |||  |   || | ||| | ||  ||  | || ||  ||| | |  | |  |  ||   | |||||||||||||||||||||||||  ||| || |||||||||  | |||| ||  | || ||  | |||||  | ||  |||| || ||||| ||  |  || 
atcaaagcagtactagcaattaattgaaaggtgactggactgaacgaaca-gcatcaacag--taattagtaatggtttgcacgcatatatatatacacgcagGGAGATCATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGATGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCGGCGGCCAGC-

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
---------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggcta----tgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                  ||||||      |   | |   |            | | ||||    |  |  ||  |||          ||||   ||  ||| |||||||||||||||||||||||||||   |||||||| |   |||| ||  | || ||  | ||||| |||||  |||| || |||||  |  |||| 
tatacactgatgatgaacagctttactgaatgcaggtagccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttg--tttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
---gtaagctttcgcttctttcgctgttcttgcatggatcga--taggctatgttgtcatc-------ttttctcataaactttgatct-----tcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
    || |||     ||  || | |  | |||   | |  ||  | |||||  | || ||        | |  | || |   |||  ||       |||||||||| |||||||||||||||||||| ||||||||||||    | ||  |  | || ||| | || ||  | ||  |||| || || || ||  | |||
gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
---------gtaagctttcgcttcttt-------cgctgttcttgcatggatcgataggctatgttgtcatcttttctcataaactttgatct--tcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
          |||||||| ||   | |        |||  |  |  ||   |    ||  |||   | ||  | |  | || |   |||  ||  |  ||||||||| |||||||||||||||||||| ||||||||||||    | ||  |  | || ||| | || ||  | ||  |||| || || || ||  | |||
atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataa-gacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA01G28310.1 (Glycine max), 3'ss of exon 6
--gtaa--gctttcgcttctttcgctgttcttgcatggatcgatag-gctat-gttgtcatcttttct-cataaact----------ttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
   | |    | |   |  | |   | || ||      ||   ||    |||  || | ||||||| | |||||  |             |   |  ||| ||||| ||||| || |||||||||||||||||||||||||   ||||  |  | || ||  | ||||| |||||  | ||  | ||||| ||    || 
ttattattattattattattattattattattattattattattattattattattattatcttttgtgcataaggtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCAGCTGTCGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA03G09100.1 (Glycine max), 3'ss of exon 6
--------gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttct-cataaact----------ttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
          ||  ||    |||  |     || ||     |||   ||   | | | |  ||||||| | |||||| |             |   |  ||| ||||| ||||| || |||||||||||||||||||||||||   ||||  |  | || ||  | ||||| |||||  | ||  | |||||||||   || 
ccaattctagaaatttcaatttcaatgttaatttttattgtgattattattttttatag--atcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
--------gtaagctttcgcttctttcgctgttcttgcatggat--cgataggctatgttgtcatcttttctcataaac------tttgatctt--cccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
         ||| |||| |||  |||   |||| ||  |   ||   ||||  ||     || |  |  |    | ||       | || |  |  | ||||||||| ||||||||||||||||| || ||||| ||||||    | ||  |  | |||||| | || ||  | || ||||| || || || ||  | |||
aatattccttaaacttt-gctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
--------------------gtaagctttcgcttctttcgctgttcttg-catggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                     ||  | ||      |   | | || ||  | |  |   | |   ||  |||     |      |       || |   | ||||||||| ||||||||||||||||| || ||||| ||||||    | ||  |  | |||||| | || ||  | || ||||| ||||| || ||  | |||
aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataag---acgtgtgctggtga-cacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagc--tttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttctcataaactttgat----cttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
|||||   |||   ||  || |      |   |||| |  ||        |    |  | |       || |||||       |   |||||||| |||||||| |||||||| || ||||||||||||  | | |||||  | || ||||| || ||  | ||  | || || || |||||  | || 
gtaagtattttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatagGGAGATAATGCACGCTATGTGGAAACCGCAAAAGTTCAAGGCGATATATCTACTAGCGACCATATATGTACTAACGCTAACGCTACCATCCGCGTCTGCG

upper sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtaagctttcgcttctttcgctgttcttgcatggatcgatag-gctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                 ||    |       |||   | |   |||||  |||  ||  ||  |  ||| |  | |  | | |     |     |   |||||||| ||||| ||||||||||||||||||| |||||||    | ||  |    || ||  |||| ||  | ||| | ||||| ||||| ||  | || 
atctttgttatgcaacatatatatataaacgtttaaatctatatgcataaatctgtattgcagttatgtgaaatctgattagaggtgatttatgttatagGGAGATAATGCATGCGATGTGGAAGCCCCAAAGGTTCAAGCTAATATACTTGACAGCAACTCTCTATGTGCTGACCCTAACACTGCCGTCAGCTTCCGCT

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: 35 (upstream exon), 35 (downstream exon)
Score: 27

GCGGACAATGTCAAGCACACTGGAGCGAGCAAACTGGTGCTCTACTTCACTGGAGCCACAAACATACTCTATACATTTGGAGGCCATGCGGTGACTGTgtaagctttc ... atcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
                                        ctttgat  putative branch site (score: 27)
                                              tcttccc  CT-rich tract
                                   ataaacttt  TA-rich tract