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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG

Basic information

species Selaginella moellendorffii
transcript EFJ16976
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g15010.1 (Oryza sativa), 3'ss of exon 1
-------------gtaagcgaatttcttggaatttcctcctctaggtcatggatctgg---ggattgcgcct---gcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
              |      ||   | |  ||||   |   |  |   ||| ||||    |  ||| |  |   | |||| | ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || || ||  | || || ||||||||||
gtaggtcgcccggatcgatcgatcgatcgagatttgtactgatttggt-tggttctgatttgtgttgggatttgggtgcagCGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAGGCCTTCGACCTCGGCGGCCACCAGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g23620.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------------------gtaagcgaatttcttggaatttcctcc-tctaggt-----catggatctggggattgc--gcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                                                 |      |||| | | || |  ||| |||  ||     | ||  |  | |  | |   |   | ||||||  | || |||||||||||||||||| ||||||| ||||||||||| |||||||| |||||||||||||| || || ||| | || || ||||||||||
gtaccctcctacccttcgcccggatctctctcccctcccccacaaccccagatctgacccgatccatttccctttcgttggatctgatccgtctgtgtttgtgcgtgcgtgcgtgcgtgggcggatggtgcagAGGTTGGTGCAGCACCAGCCGACGCAGCACCCGACGTCGGAGGAGCTCAGCATCGGGAAGATCAAGTTCAAGGCCTTCGATCTCGGCGGCCACCAGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os06g12090.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgcgcc-------tgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                || ||   |      || | | |       ||| |||| |    ||  || |         || |||||  || |    |||||||||||||||| ||||||| ||||||||||||||||||||   ||||| |||||| ||||| ||  | || || |||| |||||
tgatgatatcaaaagctactcctagattcatatatgcctgtgctcatgagtgttcattgtgtggtgatggctggttgggctgtgttgtgtttgtgtgcagAATCTGGCGGTGCACCAGCCGACGCAGCACCCGACGTCGGAGGAGCTGAGCATCGGGCGGATCAGGTTCAAGGCGTTCGACCTCGGCGGCCACCGGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os12g37360.1 (Oryza sativa), 3'ss of exon 1
------------------------gtaagcgaatttcttggaatttcctcctctaggtcatggat----------ctggggattgcg--cctgc--gcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                         || |  ||||  |  || | |   | |||   |  || ||           ||||  ||| |  ||| |  ||||||| | || ||||| || || |||||||| ||||| || || ||||||||||| || |||||||||||||| ||||||||||| ||||| || || || |
atattgaagcgatgcaaggaaatcatatgaaaattattatgattatttgcttctgtttactgaataagttggtaattgggatttgtgttccttctggcagAGATTGGTGCAGCATCAACCTACGCAGTATCCGACTTCTGAAGAGCTGAGCATTGGGAAGATCAAGTTCAAGGCGTTTGATTTAGGAGGCCATCAAATTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G086636_T03 (Zea mays), 3'ss of exon 1
-------------------------------------------------gtaagcgaatttcttggaattt---cctcc-tctaggtcatggatctgggg--attgcgcctgc-gcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                                    |  | ||    |  | ||    | ||| | |   |    |||| |      |  ||   || |||| |  | || |||||||||||||||||| ||||||| ||||||||||| ||||||||||||||||||||||| || || ||  | || || ||||||||||
gttcgtcgccgtcccccgcctgcttcccgtatcctagatctgaccgcacccgattggatcctgtccatttctggcttccgtttgcctttctgatccgttcttgtctcgatcgctgcagCGGTTGGTGCAGCACCAGCCGACGCAGCACCCGACGTCGGAGGAGCTCAGCATCGGCAAGATCAAGTTCAAGGCCTTCGACCTCGGCGGCCACCAGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G038356_T01 (Zea mays), 3'ss of exon 1
------------------------gtaagcgaatttcttggaatttcctcctctaggtca--tggatctggg---gattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                            |     |       || | || | || ||       |||| | |   | ||    |   |||| |  | || |||||||||||||||||| ||||||| ||||||||||| ||||||||||||||||||||||| || || ||  | || || ||||||||||
gtacgccaccgtcccccgtctgcttccggtatcctatcctagatctgcttccctgggcttgcctgatccgtgcttgtttcgatcgttgcagCGGTTGGTGCAGCACCAGCCGACGCAGCACCCGACGTCGGAGGAGCTCAGCATCGGCAAGATCAAGTTCAAGGCCTTCGACCTCGGCGGCCACCAGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G122666_T01 (Zea mays), 3'ss of exon 1
-------------------------------------gtaagcgaatttcttggaatttcctcctc---taggtcatggatctgg--ggattgcgcctg-cgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                     | |  | | | |  |    ||||  | |      | |    |||||||   ||||| |     ||||| | ||||| ||||||||||||||||||||||| || || || ||| |||||||||||| |||||||||||| ||||| ||  | || || ||||||||||
gtcctctctacctccgacatccgccccttttccttgcgaattccagtcttatatgctttcgacttaacggggattcctgatctggttcgattgggttcatcgcagCGGCTCGTACAGCACCAGCCGACGCAGTACCCCACGTCAGAAGAGTTGAGCATCGGCAGGATCAAGTTCAAGGCGTTCGACCTTGGGGGCCACCAGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G181536_T01 (Zea mays), 3'ss of exon 1
---------------------------------------gtaagcga--atttcttggaatttcctcctctaggtcatggatctgggg------attgcgcc----------tgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                       | |   ||  |||||||      | |    |  | |  || |    ||         || | |          |  ||||||  |    ||||||  ||||||||||  |||||| ||||||||||||||||||||   |||||||||||| ||||| ||  | || || |||| |||||
gtacacattctggcgccctggttttgcttgctaccacatgcagttgatgatttcttctcgcgtgccggccgggatagtgaacaacggtcgccctgctgtgtcgtcgttgtgctatgcagAGGTTGAGTCAGCACGCGCCGACGCAGCTCCCGACGTCGGAGGAGCTGAGCATCGGGCGGATCAAGTTCAAGGCGTTCGACCTCGGCGGCCACCGGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA09G04290.1 (Glycine max), 3'ss of exon 1
------------------------------------gtaagcgaatttcttggaa---tt--tcctcctctaggtcatggatctggggattgcg---cctg--cgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                     |     ||||| |   ||   ||  |  || |  | |  |   |  | |   ||  |     ||   ||||||| | || |||||||||||||||||| |||| || ||||||||  ||||||| || ||||||||||| || || || |||||||| || || ||  | |
gttacctttccctctctctcttacccttctcattttttttttcaatttttgaaaaaaattgattttcttaaaagaaaaaaaaattgaatttttgaaatttggttgcagAGATTAGTTCAGCACCAGCCGACGCAGCACCCCACTTCGGAGGAATTGAGCATTGGGAAGATCAAGTTTAAGGCTTTCGATTTGGGGGGCCATCAAGTTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA07G37070.1 (Glycine max), 3'ss of exon 1
----------------------------------gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                   | |   |  || ||  | | |  |    |   |  |   | |      |||   |||  ||||| | || |||||||||||||| ||  |||| || ||||||||  ||||||| || ||||||||||| || || ||||||||||| ||||| ||  | |
gtgaggttcctctcccttaacatcaaaatatcaaatcaaatacctttttttattattattaatttttttttcatttttttcgatgcaattgc--agAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGCATTGGGAAGATCAAGTTTAAGGCTTTTGATTTGGGGGGTCATCAAGTTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA19G41670.1 (Glycine max), 3'ss of exon 1
------------------gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgc-gcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                   |    |  |  |      ||| |   | |   | ||   | |    |  |  |  |  ||||||| | |||||||| ||||| || ||||| || || ||||||||| |||| || || ||||||||||| ||||| |||||| | || ||||| ||||| |
gttttgttttccttttttttttttgtttccccaatcgtttaccttttttttttattattattataagagttggttttgcagAGATTAGTCCAGCATCAGCCTACCCAGTATCCTACATCGGAGGAGTTGAGTATTGGGAAGATCAAGTTTAAAGCTTTTGATCTAGGGGGTCATCAGATTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA17G03540.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------gtaagcgaatttcttggaatttcctcctctag---gtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                                  ||     |||| ||  | |||  ||   ||    ||  |   | |   |||   ||    ||||||| | || |||||||||||||| ||  |||| || ||||||||  ||||||| || ||||||||||| || || ||||||||||| || || ||  | |
gtgaggttcctctcccttatcatcaaaatatcaaatcaaatacccttttttatttttattttttttatttttatctattaaaaagttttaattttttcgat---gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGCATTGGGAAGATCAAGTTTAAGGCTTTTGATTTGGGGGGCCATCAAGTTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA15G15330.1 (Glycine max), 3'ss of exon 1
-----------------------------------------gtaagcgaatttcttggaatttcctcctctaggtca----tggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                          |   | ||||| |   ||           |    |    || || |  | | |  |  |||  ||||| | || |||||||||||||| ||| |||| || ||||||||  ||||||| || ||||||||||| || || || |||||||| || || ||  | |
gttaccttcctccctctcctctcttacccttctcatttttcttcttccaatttttgaaaaaaaaaataagaaaaaaaaaattgaatttttgaaatttggttgc--agAGATTAGTTCAGCACCAGCCGACCCAGCACCCCACTTCGGAGGAATTGAGCATTGGGAAGATCAAGTTTAAGGCTTTCGATTTGGGGGGCCATCAAGTTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA20G38360.1 (Glycine max), 3'ss of exon 1
------------------------gtaagcg-aatttcttgg------aatttcctcc----tctaggtcatggatctg----gggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                         | | |  | ||| ||||      ||| | | ||    | | ||| ||   | |     |||| |     || ||||||||| || ||||| ||||| || ||||| || || || |||||| |||| || || | ||||||||| ||||| |||||| | || ||||||||||| |
ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaatgggaatttatttg-gcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G28910.1 (Glycine max), 3'ss of exon 1
--------------------------gtaagcg-aatttcttggaattt---cctcctctaggtcatggatct----------ggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                           | | |  | ||| ||||   |      | | |  ||| || | | |          | | |||| |  || ||||||||| || ||||| ||||| || ||||| || || || |||||| |||| || || | ||||||||| ||||| |||||| | || ||||||||||| |
tactttgtaatgtctaccttcctgacattatcatagtttattggggctaaaatatgcgcctggttattggtatttttttaaatgagaattg-gtttg-gcagAGACTAGTTCAGCATCAGCCTACACAGTATCCAACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv07s0005g01330.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------------gtaagcgaa--tttcttggaatttcctcctctaggtca-------tggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                             | ||  | |  ||| |||   | |  |  |||    ||       | | |||  ||| ||    | |  ||||| | || ||||| |||||||| ||||| ||||| ||||| ||  |||| || || || ||||||||||| || || |||||||||||||| ||||| |
gtgtgttttgattctctacagttttccttttcttttcccggggaagcaaatggagttttgttgttttattgttttctgtaccaatcttgattgttctttggactgtttttac--agAGATTGGTTCAGCATCAGCCGACTCAGTATCCGACGTCGGAAGAATTGAGTATTGGGAAAATCAAGTTCAAGGCCTTCGATTTGGGAGGTCATCAGATTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv14s0060g01340.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                       ||    || ||| |||   | |  |  | | | | || | | | || ||||    |  ||||||| | || |||||||||||||| |||||||| || || || ||| |||| || || || |||||||| || || || ||||||||||| || ||||| |
aacgattcgaattcctttttcttttcgccatttcgaggagtggatga-ttttttgttttatgtttgtttggttaattggtgttggcattggagttttgcagAGATTAGTTCAGCACCAGCCGACCCAGTACCCAACATCAGAAGAGTTGAGTATTGGGAAAATCAAGTTTAAGGCATTCGATTTGGGAGGGCATCAGATTG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S183_17V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                          ||| | | |   |||  ||   | || |     |     |     |||| |    | |||||  | | ||| || || |||||||| || || || ||||||||| |||| ||||| || |||||||||||||| |||||| |||| |||||||||||||
gctgaagcgcgataattggtgcgattgtgtagcggctcgatcaagtggaatcggtgg--ttcttttcttttcactaaattgcatcctattgtggtgacacagAGGTTGGCCCAACATCAACCGACGCAATATCCTACTTCGGAGGAGTTGAGTATCGGAAAAATCAAGTTCAAAGCATTTGATCTGGGTGGTCACCAGATCG

upper sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S7_338V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------gtaagcgaatttcttggaatt--tcctcctctaggtcatggatctggg---gattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
                                 || |   |||  | || ||    |  |  |    ||||   |  ||      | |  |      |||||  | | |||||| || |||||||| || || || ||||||||| ||||||| || || || |||||||||||||||||  |||| |||||||||||||
gtaaggaagtgcgatgaatggagcggttggtgagtgatgcaatgccgtgaaaccggttgtttttcctgtcactaaattgcatcctactatggtgatacagAGGTTGGCCCAGCATCAACCGACGCAATATCCTACATCGGAGGAGTTGAGCATTGGAAAAATTAAGTTCAAAGCGTTTGACCTGGGTGGTCACCAGATCG

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), 35 (downstream exon)
Score: 29

CTTAGCGAGCCTAGGGCTGTGGCAGAAGGAGGGCAAGATCTTGTTCCTAGGGCTCGACAACGCCGGCAAGACGACGCTGCTACACATGCTCAAGGACGAGgtaagcgaat ... gcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcttggaatttcctcctctaggtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG
          aattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgaatttcttggaatttcctcctctaggtcatggatctggggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA