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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagaagaaaacacattgtggtctgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

Basic information

species Selaginella moellendorffii
transcript EFJ04980
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
----------------gtatgaagaagaaaacacattg-tggtctgagctcaaacttagt-aacgtc------catgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                  |     |   |  || |||| | |||   ||| | |     |  |||        |||||| ||||||||| |||||||||||||||||||| || || || || || || || ||  |  |||||||||| || ||  |||| ||    ||||| || 
gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgat-gcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
----------------------------------gtatgaaga-agaaaacacattgtggtctgagctcaaacttagtaacg---tccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                  | |||     |  ||| ||||| ||   |     | ||||   ||||    | ||  ||  |||||||| ||||| ||||||||||||||||| || || ||||| || || |||||  ||||||| || || ||  |||| |||   |||||||| 
gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
----------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                    |      ||||  ||  |||||||| |    | |  | |  |    |          ||||||||||||| ||||||||||||||||| || || || |||||||| ||  || | ||||| || || ||  | || |||   |||||||| 
gttcaacatctccaaaaattttatcagttgttttccactctacagaag-cagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6
-------------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                       |      ||||   |  |||||||| |    | |  | |  |    |          ||||||||||||| ||||||||||||||||| || || || |||||||| ||  || | ||||| || || ||  | ||  ||   |||||||| 
gtacaacatctactctgaaaattttatcagttgttttccactctacagaag-tagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
----------------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                          |      ||||  ||  |||||||| |    | |  | |  |    |          ||||||||||||| ||||||||||||||||| || || || |||||||| ||  || | ||||| || || ||  | || |||   |||||||| 
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaag-cagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
------------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaac--ttagtaacgtccatg-atcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                      |      ||||   |  ||||| || |   || |  |  ||  |  | |   ||      ||||||||||||| ||||| ||||||||||| || || || |||||||| ||  || ||||||| || || ||  | || |||   |||||||| 
ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaag-tagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------------------------------gtatgaagaagaaaacacat-tgtggtctgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                                                                      |  |||| | |||  || | |   ||||      ||| ||  | |  | |||  | ||||||||||||||| ||||||||||| ||||| || || || || ||||| || ||  | || || || || ||| ||||  ||   |||||||| 
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgat-tacatt-ttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------gtatgaagaagaaaacacattg-tggtctgagctcaaacttagtaacgtccatgatc-------gcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                                             |      |            || ||| |  | | | | | |   ||   | ||        | ||||||||||||| |||||||| ||||||||||| || ||||| ||||| || ||  | || ||||| || ||  |||| |||  ||| || |||
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

upper sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 3
------------------------------gtatgaagaagaaaacacattgtggtctg-----agctcaaactta---gtaacgtccatgatc--gcagGATTTTAAGATCCAGAACATTGTTGGCT--CCTGCGACGTT-AAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC----
                               |  |  | |     |  | |||||  ||      || ||  |||    | |   | | || ||  |||| |    |||||     | |   | ||||  ||||| ||||| |||      |  |      |   | |||  | |  | |||   | ||| | | |    
aggcgggggcatgatgggctaccaaacgcacttcgttggaagccgctgaatgtgggttgcatgtggcgcatccttgcatgcatgttgcttggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTTAAGATCCAAAACATCGTGGGCTCCTGTGACGTCAAGTTCCCCATCCGCT

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|169065931|gb|FE475379.1|FE475379
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169034024|gb|FE444214.1|FE444214
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169065615|gb|FE476181.1|FE476181
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169081802|gb|FE488260.1|FE488260
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169078386|gb|FE488261.1|FE488261
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169027385|gb|FE432682.1|FE432682
EST:     TATGCTCGCATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169034025|gb|FE444215.1|FE444215
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTNAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169027384|gb|FE432681.1|FE432681
EST:     TATGCTCGCATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169044778|gb|FE451922.1|FE451922
EST:     TATGCTCGCATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169027778|gb|FE433238.1|FE433238
EST:     TATGCTCGCATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169108645|gb|FE509768.1|FE509768
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169108646|gb|FE509769.1|FE509769
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
EST: gi|169065616|gb|FE476182.1|FE476182
EST:     TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAA                         GATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC
genomic: TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATC

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: 32 (upstream exon), 33 (downstream exon)
Score: 45

TATGCTCGTATCATCCAAAAGCTGGGATTCCCCGCACAGTTTAAAgtatgaagaa ... atgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaagaaaacacattgtggtctgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
                                  tagtaac  putative branch site (score: 45)
                             aaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaagaagaaaacacattgtggtctgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG