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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacgtgttttttttctttgtgcgcgtttgtttttcctaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA

Basic information

species Selaginella moellendorffii
transcript EFJ20767
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 4
---------------gtgacgtgttttttttctttgtgcgcgtttgtttttcctaaccact-ttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
               ||  |  ||| | | |  |||    | |   |  ||| || | |   ||  |   ||||||| || ||||| |  |||||| |  | || ||||| ||| | ||||||||||||||||| ||||| || |||||||| ||||||||||| ||||| || |
gtgcttttctacaatgtttcaagttctgtcttattggaaacctgcttcgttcttatcaatagtttttgggtgcagATACACACATCTAAGATGACATTGGCAGATGATGTTAACCTAGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 3
---------------------------------gtgacgtgttttttttctttgtgcgcgtttgtttttcctaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                                     | || |   |        |  | |||| || || | |    | ||  || ||||||| || ||||| |  |||||| |  | || ||||||||| | ||||||||||| ||||| ||||| || ||||| || ||||| ||||| ||||| || |
gtaaatatccattagtatcttttagaacttcagaatgcatgataactgataagcagttcctttggttctcatgaatgttgtgaatcgtgcagATACACACATCTAAGATGACATTGGCAGATGATGTGAACCTGGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 3
----------------------------gtgacgtgttttttttctttgtgcgcgtttgtttttccta-accactttg---gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                             ||   |     | |||||  | | | |||||| ||  || |  |  |||     |  ||||||| || ||||||| ||||||| |  |||| ||||||||||| ||||||||||| ||||| || ||||| ||||| || ||||| || |||||||| ||||
gtactgtgacgtctgtaaatgataatatttgcattaacaatgttcttaataccc-tttgttcttattatagaaggttgtaaacttgtgcagATACACACATCGAAAATGACATTAGCTGATGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGACGAGTTTTCGGGTGCTGATATTAAGGCAATCTGCA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
----------------------------gtgacgtgttttttttctttgtgcgcgtttgtttttcc--taaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                             ||   | |   | ||| |  | |   |||||  ||    | |    | |    | ||||||| || ||||| | ||||||| |  |||||||||||||||| ||||||||||| ||||| || || || || || || ||||| || ||||| || ||||
gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtgacgtgttttttttctttg--tgcgcgtttgtttttcctaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                                           | || ||  |  ||| ||         | || |   | || |  |||||||   |   |||| || |||||||| |||||| |  |||| ||||| ||||| ||||| ||||| ||||| || || ||||| ||||||||||| || |||||||| || |
acccaacataagatgttgtttctgctgattctatgtgatatcttaacatgcatactttgttcaatcatatgcttatacattctcat-actttggaatta--agATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------gtgacgtgttttttttctttgtgcgcgtttgttttt----cctaacca--ctttggtt-cttgc-------agATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                   | | || || ||| | ||| || |  |||  |        || | |    |||  || | |||       |||| || ||||| |  |||||  |  |||| ||||||||||| ||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------gtgacgtgttttttttctttgtgcgcgtttgtttttcctaaccactttggttcttgc---------agATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                      || |   |   |    | |  |    ||| || ||| |      | ||| |  ||          |||| || |||||||  ||||| ||||| || ||||| ||| | |||||||||||||||||||| ||||| || || |||||||| || ||||| || ||||
gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA

upper sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------gtgacg--tgttttttttctttgtgcgcgtttgtttttcctaacca-----ctttggttc---ttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                                                            |||||   ||  |           ||  | ||  | || |||| ||     | ||  ||    |||||||| |||||||| || |||||| |  |||| ||||| ||||| ||||| ||||| ||||| ||||| || |||||||||||||| || |||||||| ||||
gtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

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|169046394|gb|FE457398.1|FE457398
EST:     AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAG                         ATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
genomic: AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
EST: gi|169065781|gb|FE474371.1|FE474371
EST:     AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAG                         ATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
genomic: AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
EST: gi|169113680|gb|FE514786.1|FE514786
EST:     AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAG                         ATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
genomic: AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
EST: gi|169060659|gb|FE467397.1|FE467397
EST:     AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAG                         ATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
genomic: AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
EST: gi|169040852|gb|FE447903.1|FE447903
EST:     AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAG                         ATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
genomic: AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
EST: gi|169046408|gb|FE457399.1|FE457399
EST:     AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAG                         ATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT
genomic: AAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTT

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: 34 (upstream exon), 33 (downstream exon)
Score: 16

CATCGAAAGCTTGGACCCTGCGTTGCTTCGACCCGGTAGAATTGACCGGAAAATCGAGTTTCCTTTGCCGGATATCAAAACCCGACGACGCATTTTTCAGgtgacgtgtt ... gttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgttttttttctttgtgcgcgtttgtttttcctaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA
                               tcctaac  putative branch site (score: 16)
                                              ttcttgc  putative PPT
     tttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacgtgttttttttctttgtgcgcgtttgtttttcctaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA