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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

Basic information

species Selaginella moellendorffii
transcript EFJ31084
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
----------------------------gtctgtgtg-tttgttatttgctttttttctttgtctaacgaa-----------------tttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                             | | | || | | || |||  |||||    |||| | || ||                 |||||    ||||| |||| |||  || |  | ||||| || || || || || ||||||||||||||||| || ||||| ||||||||||| || ||||| ||||| || |
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 21
-----------------------------------------gtctgtgtgtttgttatttgctttt----tttctttgtctaacgaatttat-atggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                          | | | |   | ||||||| |  |    |  ||||   ||  |  | | |  || ||||| ||||  ||  || |  | ||||| || || || || || ||||| |||||||| || || || ||||||||||||||||| |||||||| ||||| |
gttatgaatggatgggggtactacttttggatagtggaattttttatttccattttatttgatagtgaactgacttttgttattgcttatgttgtgccagCCATGTAAAGGAATATTACTTTTTGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATAT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                               ||||  |     |  | |||   |  ||  || |  | |   | | |    ||||| ||||  ||  || |  | |||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||||| || |
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctg-atcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
---------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtcta-acgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                               || |  | |        |||   ||   |||| || |     || |||  ||||| ||||  ||  |  |  | ||||| || || || ||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| || || |
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 21
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtct---aacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                               |||    || ||| |   |||| || | ||  |   ||  |  ||  ||| ||||| || | |||  | || ||||||||||| || ||||| |||||||| |||||||| ||||| |||||||| || |||||||||||||||||||| ||||
gtaaaaatcacaaacattaaaataatgtgaagttgtagcccatctcttgtcaaattattaatcatttttattttatgattgtgaattaccttccatg-cagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtc-taacgaatttatatg---gcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                           ||| |       |||||  | |||||   ||||  |   |||||    |    |||||| || | |||  | || ||||||||||| || ||||| |||||||| |||||||| ||||| |||||||| || |||||||||||||||||||| ||||
agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttg--tctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                             | | |     | ||||    | | ||   | |  ||| |   |  | |   |||||| || |  ||  | || ||||||||||| || ||||||||||| || |||||||| |||||  ||||||| || |||||||| || |||||||| ||||
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtct---aacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                             | | |     | ||||    | | ||   |   ||   ||  |  || | || ||||| || |  ||  | || ||||||||||| || ||||||||||| || ||||| || |||||  | ||||| || ||||||||||| |||||||| ||||
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtg-cagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                                  | ||  || ||   || ||  |     |  ||       | | ||   ||||||||||  ||  | ||||||||||| ||| | |||||||| |||||||||||||| ||||| || || || || |||||||| ||  ||||||| || |
aatttggctttcctcaaaaaatttatctcctataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctaca-cagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                                  | ||  || ||   ||  |  |        |||      | | |||| ||||||||||  ||  | || |||||||| ||||| |||||||| |||||||||||||| || || || || |  || |||| ||| || |||||||| || |
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatg-cagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------gtctgtgtgtttgttatttgctttttttctttgtctaa---cgaatttatat-----------ggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                      | | ||||||| ||| |  |  |   |  || |   | ||  |||||            |||||||   |  ||  |||| || ||||| ||||| || ||||| ||||| ||||| || || || || || || |||||||| ||||||||||||||||| |
gtaccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
----------------------------------------------gtctgtgtgtttgt-tatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                               ||| ||   |||| |  |         |||| || |||    |  || || |||||||| | |||| ||||  ||||||| || || ||||| || ||||| |||||||||||||| |||||||| || ||||||||||| |||||||||||||
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtg-cagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

upper sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
-------------------------------------------------------------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                                                                                  |||   |   ||   | |   | | |  | ||  | | |    ||| |  |||||||| | |||  | ||  ||||||| ||||| || ||||| || || |||||||| ||||||||||| || ||||| ||||||||||| ||||| || |
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatcta-attcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

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), 33 (downstream exon)
Score: 20

TCACATTGGTGCTTTGGATAATGTGAAAGAGACCCTACGCGAGCTGGTGATGCTTCCATTACAACGGCCAGAGTTATTCGTCAAAGGCCAACTTACGAAGgtctgtgtgt ... tatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
                                 gtctaac  putative branch site (score: 20)
               ttatttgcttttttt  TA-rich tract