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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC

Basic information

species Selaginella moellendorffii
transcript EFJ08612
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G114126_T02 (Zea mays), 3'ss of exon 2
---------gtaagtcttcccttgttctttt-tcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacg------atcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
          ||||       | ||| |    || | | |||  | | || || |   |  |  ||   | | |     | ||  |      ||    |||||||||| ||||| ||||| |||||||||||||| || ||||| || || || ||  | |||||||| |||||  | ||||||||||| ||||| ||||
tctatggttttaaggtcatagtagttttacgatcgtatacttgaagttctggtctgattcaggatcactattttaacaaccttgtgtggttaatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
---------gtaagtcttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacg--------atcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
         || |   | |   | ||   | || |   |||  | | || |   |  ||      | |  |||||     | | |        ||    |||| ||||| ||||||||||| ||||||||||| || || ||||| || || || ||  | |||||||| |||||  | ||||||||||| ||||| ||||
atcgtagtagttatgatccaactatttactatcctacacttggagttct-gacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 2
------------------gtaagtcttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
                  ||     ||       |  ||||| | |   || |  |  | |  || | ||  |  | | |   |  |  ||||  |  | |||| || || || ||||||||||||||||| |||||| |||| || ||  |||| || ||||||||||| |||||| | |||||||| || ||||| ||||
tttctattttatctcatggtggactttggaaaaattattttcctctatatttataatgtatcatt-tctgcatgtttatttcctt-tacttacactttacagGAGCGAGATAGTTACTGGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCAGTTATCATTTTTGAACCAATGACAATGC

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 2
-------------------gtaagtcttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
                   || |   ||      ||  ||||| |     || |  |  | |   | | ||  |  | | |   |  |  ||||  |  |||||| || ||  | ||||||||||||||||| |||||| |||| || ||  |||| || ||||||||||| || ||| | ||||||||||| ||||| ||  
atttttattttatctcatggtgaactttggagaatttcttttcctccatatttataatgtatcaat-tctgcatgtttatttcctt-tacttacacttaataGGAGCGAGATGGTTACTGGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCGGTTATCATTTTTGAGCCAATGACAATA-

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 2
-------gtaagtcttcccttgttctttttcttgttctttca-----atactt-----gtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
        |      | |||||   | |  ||  ||| | |      ||| |       || || | | |||  || | ||||||   ||   ||  | ||||  | ||  | |||||||| |||||||| ||||||||||| ||||| || || || ||||||||||| |||||| | || ||||| || ||||| ||| 
gatttcccttttctcttccttggcatatgcctcattcatacgtgctcatattctgaacattattatctcttttttctccctttggctcttgt-atataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACACTACCAGTTATTATATTTGAACCAATGACTATGA

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
-gtaagtcttcccttgttctttttcttgttctttcaatacttgttt---------ttgtttgtttcctcactctttggtctttacga------tcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
  |  || || | || || | | | ||  |  ||||  || |   |         ||  ||||    | | | |||  | | |  ||      |  | ||||  | ||  | |||||||| ||||||||||| |||||||| || || || || || ||||| ||||| |||||| | |||||||| || ||||| ||||
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 2
----------------gtaagt-cttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
                | |  | | ||  |  | | |  || | ||||     |   | || || | | |||  || | ||||||   ||   ||  | ||||  | ||  | |||||||| |||||||| ||||||||||| ||||| || || || ||||||||| | || ||| | || ||||| || ||||| ||| 
ctttttctcttccttggcatatgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgt-atataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaagtcttcccttgt----tctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcg---atagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
          | | |   ||  | |    || | || | |   |||      |  ||||| |||||      | | |  | |  ||  | |      |||||  | || || |||||||| |||||||| |||||||| || || || ||||| || ||||||||||| |||||| ||||||||||||| ||||| ||||
aatcttgtcttgaattacccgatatgaaatcatattttagcaatttatcctgtattttttatttgtgctgatattttgagcttgttctgttttcttgtagGAAAGGGACAGTTACTGGAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGC

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtaagtcttcccttgttctttttcttgttctttca-atacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
                      ||          | |  | |   | || || || ||  || ||  || |  |||  |   |   |  | |||    ||   |||| || || || |||||||| ||||||||||||||||| || || || ||||| || ||||||||||| || ||| |||||||||||||  |||| || |
atggagtgataaattgggggaaaaagaaaagaaggcttctctgtatatttttacatatggttattgatgctcattttttgggt---taattttttttttc--cagGACCGGGACAGTTACTGGAAGATGATGCACAAGTATATAGGCTCTGATGTCACATCAATGGTGACACTTCCTGTTATGATTTTTGAGCCGTTGACTATAC

upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------gtaagtcttcccttgttctttttc--ttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgat----cga---tagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
                                                                                               |     |    |   || | ||   || |  | | ||    |   |   |  | | ||| ||  || ||| |||   ||    | |    ||||| | || || || |||||||||||||||||||| || || || ||| | ||||| ||||||||||| |||||  | || |||||||||||||| | ||
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC

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|169060494|gb|FE469000.1|FE469000
EST:     GCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAA                         GATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTC
genomic: GCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAAgtaagtcttc ... cgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTC
EST: gi|169050791|gb|FE459937.1|FE459937
EST:     GCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAA                         GATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTC
genomic: GCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAAgtaagtcttc ... cgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTC
EST: gi|169025463|gb|FE436077.1|FE436077
EST:     GCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAA                         GATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTC
genomic: GCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAAgtaagtcttc ... cgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTC

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: 47

TATGCTGGGCGGCGTGGAGGGTCTAGAGGTTATCAATCCCGAAGGCGGCCAAGAGGATGCCGAGAGCGAAGCACTCAAAGGCCGCTTCAAGCAAGAAgtaagtcttc ... cgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
                         tcctcac  putative branch site (score: 47)
                                       tctttac  putative PPT
             tttttgttt  TA-rich tract