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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcttgctctatcgttgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

Basic information

species Selaginella moellendorffii
transcript EFJ08844
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
-----------------------gtgcgcttgctctatcgttg----aa------gcgtgttgatgct-acattacttttttttt--ttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                        ||| |||| | | |  |||    ||      || | | ||  || ||||   | |||||||  |   ||   | ||||||| |||||||| ||  |||| |||||||| ||||||||||| ||||| ||||| || || || ||     | |  |   || | || || ||||| |
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
----------------------------gtgcgcttgctctatcgttga-agcgtgttgatgctacatta-------ctttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                             ||       || |   || |  |    |||| | ||  | |         |||||| | |   |     |||||||||||||||| ||  |||| |||||||||||||||||||  ||||  ||||| || || || |||   ||||  |   |||| || || ||||| |
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 3
--------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                          |  |       |||| | | |   | ||  ||  |  || | | | |  |  | | |||   |||||||||| || |||||  ||||||| || || || |||||||||||||||||||| || || ||||| || || |  ||  || | || || ||||| |
gtaatcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaatatt-tataaatgtatgatcattgtttc---agTTTGACTATCTTAAGAGTTTGGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
-----------------gtgcgcttgctctatcgttgaagcgtgtt------gatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                     | || | ||  ||   ||  |||||      | | ||  || |  ||  ||||    ||    ||||||||||| ||||||||  ||||||||||||| || |||||||||||||||||||||||  | ||||| || ||    ||| |  | || || || || |
gtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
-------------------gtgcgcttgctctatcgttgaagcgtg---ttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                    |   ||| |||     ||      |    || ||    | || | |  | | |     ||  ||||||||| |||||||||||  ||||||||||||| || || |||||||| ||||||||||| || || || || |||| |||| |  | || || ||||| |
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacattactttttttttttggcttc-cccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                                                        ||    |  || ||| ||   |     ||    |  |||     |||  | ||  |     ||||||||||| ||||||||| |||| || ||||| || |||||||| || ||||||||||| || |||||| |||| |  ||| || | ||||||||||| |
gtgtcctttaagaatttcgtttctgggttgctgatgattaccatatccttttatcttgtctgtcttccatccttactggactctggaatttaattctgcatttaatatgtttgaattcagTTTGACTATCTCAAGAGCTTGGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------gtgcgcttgctctatcgttgaagcgt----gttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                                                |  |||  ||       ||||  ||     ||||||| ||||| ||| || | | ||     | ||||||||||| || |||||| |||| |||||||| || ||||| || ||||||||||| || || || || || || |  ||| || |||| || ||||| |
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggct-ctgaaatgttttaattgatgccacattgcttattctctgtg-----ctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                                    ||   ||         ||| |   | ||  | ||| ||      | ||  ||   ||||  ||||||| || ||||||||  |||| |||||||| || ||||| || || ||||||||||| || ||||||   ||    ||| || | ||||| |||||||
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttcc--agTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacat-tacttttttt----ttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                                |||  |     | | | | || | | ||      |||  | ||||| |     | ||   ||   ||||| || ||||| |||||  |||| |||||||| |||||||||||||| |||||||| || ||  | || |  || |  ||| |  | || || |||||||
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA

upper sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------------------------------------------gtgcgcttgctctatcgt-tgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                                                                                                                               |   | |  || |||| | |  | ||||||     |||  |||| | ||| |||     |  |||||||| ||| | |||||  |||| |||||||| |||||||| ||||| ||||||||||| || || |||| |||||  ||  |  | || || |||||||
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttcttt-----ctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA

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: 33 (upstream exon), 32 (downstream exon)
Score: 6

GCAGCTAAAAAACCGCAAAGAGTTAGAAAAGGCTGACCATTCGATACCTAGGCATCCGGAGTACCGCTACTCAACAGAGTTCCAAAGCCATGAACCAGAGgtgcgcttgc ... gcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatcgttgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
                tgttgat  putative branch site (score: 6)
                             ttactttttttttttg  putative PPT
                         tacattactttttttt  TA-rich tract