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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatctttggttggtctaatctgttattaaatccag

Basic information

species Selaginella moellendorffii
transcript EFJ24508
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 24
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtt----tctggttatactctatctttggttggt-ctaatctgttattaaatccag----------------------------
||| |||||||| || || ||||| ||||| ||||| ||||||||||| || || |||||| |||| |||||||||||||||||||| || ||||||||||||    || ||       ||| |   |||  | | |   |  || | | ||| || |||  || ||                            
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttctta--tctagattttttctaacacccttttttgtatag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 24
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttc----tggttatactctatctttggttggt-ctaatctgttattaaatccag------------------------------
||| |||||||| || || ||||| ||||| ||||| ||||||||||| || || |||||| |||| |||||||||||||||||||| || ||||||||||||    || ||   |    || |   |||  | | |   |  || | | ||| || |||  || ||                              
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggaccaacctgttagaactaaaacatatttcagtacaagtcttttctta--tctagattttttctaacacccttttttttgtatag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgta----------aggctatagtttctggttatactcta-tctttggttggt--ctaatctgttattaaatccag---------------------------------
||| |||||||| || || ||||| || || ||||| ||||||||||||||||| |||||| | || |||||||||||||||||||| || ||||| ||||||          |||  ||| ||  || || | | ||| |||||| ||  |  | ||  |  ||| | ||                                     
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
------------------------------------------------------------------------GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgta-------aggctatagtttctggttatactctat-ctttggttggt--ctaatctgttattaaatccag--------------------------------
                                                                        ||| |||||||| || |||||||| || || ||||| ||||||||||||| ||| |||||| | || |||||||||||||||||||| || ||||| ||| ||       |||      |   || || | | |||| ||||| ||  |  | ||  |  ||| | ||                                    
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 1
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatctttggttg-gtctaatctgttattaaatccag----------------------------------------------------
||| |||||||| || || ||||| || || ||||| |||||||||||||| || |||||| | || |||||||| ||||||||||| || ||||| ||||||      |||   |   |  |     || ||| || |  |||  | | |     |                                                          
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 5'ss of exon 14
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatctttggttggtctaatctgttattaaatccag-------------------------------------------------------
||| |||||||| || || ||||| || || ||||| |||||||||||||| || |||||| | || |||||||| ||||||||||| || ||| | ||||||      |||   |     |||||  ||  ||  || ||   ||||| | |  |    ||                                                       
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagca---catacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GRMZM2G111355_T02 (Zea mays), 5'ss of exon 5
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatctttggttg-gtctaatctgttattaaatccag--------------------------------------------------------------------------------------------------------------------
||| |||||||| || || |||||  | || ||||| |||||||||||||| || |||||| | || |||||||| ||||||||||| || ||| | ||||||      |||   |   |  |     || ||| || |  |||  | | |     |                                                                                                                          
GGCTAACAGTGCCAAAACATGGAAGAAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagcacatacttaataattttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttaggtcgatgatgccttccttacaaagtaaatggtcctctccttgcccccagttatgatctgtttatag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactct------atctttggttggtct--aatctgttattaa--atccag----------------------------
 || |||||||| || || ||||| ||||||||||| || |||||||||||||| |||||  |  | || || |||||||| || || || ||| | |||||||     |  ||| ||  ||  || |      || ||    ||  ||  ||| |||| ||    || |||                            
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgtaatatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttctttattcagctgtcatctgatttccagttagaaagtt

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 24
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactct-atctttggttggtctaatctgttattaaatccag-------------------------------------
 || |||||| | ||||| ||||| ||||||||||| ||||||||||| ||||| |||||  |  | || || || ||||| |||||||| ||||| |||||||     |  |||| | || |    | | || ||  ||      | | |   || ||  ||                                     
AGCTAACAGTTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCGGAGGAGTTTCGTTTGGCCCAGATTTGTGGACTCAACATTATTGTTCAGgtaatatgttgatttcagtttttttgatgaactgtgtgtgtgtgtgtatatatatatatataggaacgtctttcttaatttctgatgccagaccgagttc

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 23
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactct-------atctttggttggtct--aatctgttattaa--atccag---------------------------
 || |||||||| || || ||||| ||||||||||| || ||||||||||| || |||||| |  | || || |||||||| || ||||| ||| | |||||||     | |||| | |  |     |       || ||    ||  ||  ||| |||| ||    || |||                           
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCAGAGGAGTTCCGTTTGGCCCAGATATGTGGGCTTAACATTATTATTCAGgtaatatgtttgtttgttgccaagtcttcaactaaattttgaaatgaactggaatttgtttttctttattcagctatcatctgatttacaattagaaagt

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 24
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagttt--ctggttatac---tctatctttggttggtctaatctgttattaaatccag-------------------------------------------------------
 || |||||||| ||||| ||||| ||||| ||||| ||||| ||||| || || || ||| || | || |||||||||||||| ||||| ||  | ||||| |     |  | |  |||   | |    | |  | ||    | | ||   |   |||   |                                                           
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGCGTTGATGCTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 24
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatctttggttggtct----aatctgttattaaatccag-----------------------------------------------------------------------------------------
||| |||||  | ||||| ||||| || |||||||| ||||||||||| || ||||||||| |  | || || ||||||||||||||||| ||| | ||||||| |   |  ||| |     ||   |    |       ||     |||   || ||   || |                                                                                          
GGCTAACAGCTCAAAGACATGGAAGGAGGTTTGCTTTGCTTGTGTTGATGCAGAAGAGTTCCGCTTAGCTCAGATATGTGGTCTCAACATTATTATACAGgtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 12
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctg--gttatactctatctttggttggtctaatctgttattaaatccag-------------------------------------
|||||| || ||   ||| ||||| ||||| ||||| |||||||| ||||| ||||||||| | || || ||||| |||||||||||  | |||||||||||| || ||  |||||||  |||| | | |    || |       | | |  ||   || |  |                                     
GGCCAATAGCGCACGGACATGGAAGGAAGTCTGCTTTGCTTGTGTGGACGCCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatggata-ggtttctgctgttacattttgcaattagcctcatgattttactacgcaaccatgcttttcattactatcatatgttctaatcgtactgaag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 5'ss of exon 12
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatct--ttggttggtctaatctgttattaaatccag-------------------------------------
||||||||||||   ||||||||| ||||| ||||| |||||||| || || ||||||||  | || || ||||| |||||||||||  | |||||||||||| |   |    ||||  |  | |   |||   |  |||    | |  | |   |  ||| ||                                     
GGCCAACAGTGCACGGACGTGGAAGGAAGTCTGCTTTGCTTGTGTGGATGCCGAAGAGTTTCGTCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatgaaaa-gccttctaatgcttcgacatccgatcagttttcttgagttttctgtttatcaaggttctttccttgattagtttgttgtttcatgatgtgc

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|169097272|gb|FE497649.1|FE497649
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169045878|gb|FE451734.1|FE451734
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169082005|gb|FE486448.1|FE486448
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169047382|gb|FE456215.1|FE456215
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169114799|gb|FE516060.1|FE516060
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169025122|gb|FE434709.1|FE434709
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC

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: 35

GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctatagtttctggttatactctatctttggttggtctaatctgttattaaatccag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA