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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacag

Basic information

species Selaginella moellendorffii
transcript EFJ31249
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os08g44450.1 (Oryza sativa), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattg-agcgccctctctcctttagttgc-cggattgaatcactggtccattgcttttttgcacag------------------------------
||| ||||||||||||||||||||||| || |||||||| || ||  | || ||||||||||  || |||||||| |||||||| |||||||| |  |||||||||||     ||| |  |   |||  ||      |||    |||    |  ||   ||       ||                              
GCAAAAGGACAAGCGTTTCAGCGGCTCCGTCAAGCTGCCCCATATCCCCCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCCCAGCATGTCGAGGAGgtaagattatgatgccatacccattttgattttgtaaatttgtacaccctccgtttagattgaaattgaggattttcctttctcactcatgtaagtgacc

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagat---------tgagcgccctctctcctttag--ttgccggattgaatcactggtccattgcttt--tttgcacag-------------------
 || ||||||||||||||||||||||| || |||||||| || ||  | || ||||||||||  || |||||||| |||||||| |||||||| |  ||||||||||         |   |    | | |  || ||  ||  | | ||  || | ||    |||   |   |||| |||                    
ACAAAAGGACAAGCGTTTCAGCGGCTCCGTTAAGCTGCCCCATATCCCCCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCCCAGCATGTCGAGGAGgtaagatatgatgttgtagccattttgtttaattcagactttacaggttacattattgtagtattttctcaatttgaacacatgtagtgttactgaatta

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgca-cag-------------------------------
 || ||||| ||||||||||| || || || ||| ||||||||||  | || || |||||||  ||||||||||| |||||||| |||||||| |  ||||||   |         ||  |  |  |    |    |||  |   |     ||||   ||| | |  ||                               
TCAAAAGGATAAGCGTTTCAGTGGATCTGTTAAGTTGCCTCACATCCCCCGCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtactcttttatcagttttgcatcaacttccttgtgtacataacagattgtgctttagtaatagaaaattgttgataggcttctacaatgaaggg

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G144387_T01 (Zea mays), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag-----attgagcgccctctct--cctttagttgccggattgaatcactggtccattgcttttttgcacag-------------------------
 |||||||||||||||||||| ||||| || ||| |||| || ||  | || ||||||||||  ||||||||||| |||||||| |||||||| |  ||||||||     |||||  | |  ||    | |  | ||    |  ||    ||  |   || | | ||   |  |                          
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCCCATATCCCTCGTCCCAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAGGAGgtaagcaagcattgatggtctgcttcaacatgcacttttttgtatgttgaacatgctaatggttgttgaactgaaaaaacaccagtgttttgaattattc

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G181194_T01 (Zea mays), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag------attgagcgccctctc-----tcctttagttgccggattgaatcactggtccattgcttttttgcacag---------------------
 || ||||||||||||||||| ||||| || ||| ||||||||||  | || || |||||||  ||||||||||| |||||||| ||||| || |  |||||||        ||||     | ||      |    |  ||      |||||        |  | |    | |||| |                      
ACAAAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCACATCCCTCGTCCAAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCACGTTGAGGAGgtaaacaggcagttgatgatgcacttgaaaatgtacttatttatatgttgaacatgcttgcagtagtaaatctgcaaaaacaccaatgcttcgagttact

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G023748_T02 (Zea mays), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagat---------tgagcgccctctctcctttagttgccgga-------ttgaatcactgg---tccattgcttttttgcacag-------------
 || ||||||||||| |||||||| || || ||||||||||||||  | || || |||||||  || |||||||| |||||||| |||||||| |  |||||| | |         | | | |   || |  |||  ||| || |       |||   | | ||   || |||  ||  |     ||             
TCAAAAGGACAAGCGCTTCAGCGGTTCTGTTAAGCTGCCTCACATCCCTCGCCCTAAGATGAAGGTTTGCATGCTTGGTGATGCTCAGCATGTTGAGGAGgtatgttatgcttccatcatctcgtcctgtgttttttttggcgtaaatttacttggtactcaggaattcaattatttgctcttgtagcgaatatgagctt

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G170561_T01 (Zea mays), 5'ss of exon 4
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag------attgagcgccctctc-----tcctttagttgccggattgaatcactggtccattgcttttttgcacag---------------------
 || ||||||||||||||||| |||||  ||||| ||||||||||  | |  || |||||||  ||||||||||| |||||||| ||||| || |  |||||||        ||||     | ||      |    |  ||      |||||        |  | |    | |||| |                      
ACAAAAGGACAAGCGTTTCAGTGGCTCTATGAAGTTGCCTCACATCCCTCATCCAAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCACGTTGAGGAGgtaaacaggcagttgatgatgcacttgaaaatgtacttatttatatgttgaacatgcttgcagtagtaaatctgcaaaacaccaatgcttcgagttactc

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM5G862017_T01 (Zea mays), 5'ss of exon 9
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacag------------------------------------
 || ||||||||||||||||| |||||  | ||| ||||||||||  | || || |||||||  ||||||||||| |||||||| || || || |  |||||||        ||  |   |  |  | |||    ||  | | | |  |   |||    |     |||                                    
ACAAAAGGACAAGCGTTTCAGTGGCTCTATTAAGTTGCCTCACATCCCTCGTCCAAAGATGAAGGTGTGCATGCTTGGTGATGCCCAACACGTTGAGGAGgtaaac----aggcagttgatgatgcacttgaaaaatgtacttatttatatgttgaacatgcttgcagtagtaaatctgcaaaaacactaatgcttcgagttac

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G074769_T01 (Zea mays), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag------attga--gcgccctctctcctttagttgccggattgaatcactggtccattgcttt---tttgcacag---------------------
 || ||||||||| ||||||| ||||| || ||| |||||| |||  | || || |||||||  ||||||||||| |||||||| ||||| || |  |||||||        ||||    || ||      | || ||      |||    ||  |      |   |   | |||| |                      
ACAAAAGGACAAGAGTTTCAGTGGCTCTGTTAAGTTGCCTCGCATCCCTCGTCCAAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCACGTTGAGGAGgtaaataggcagttgatgatgcacttgaaaatgtacttatttagttgttgaacatgcttgcagtagtaaatctgcaaaaacactaatgcttcgagttact

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G369991_T01 (Zea mays), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag------attga--gcgccctctctcctttagttgccggattgaatcactggtccattgcttt---tttgcacag---------------------
 || ||||||||| ||||||| ||||| || ||| |||||| |||  | || || |||||||  ||||||||||| |||||||| ||||| || |  |||||||        ||||    || ||      | || ||      |||    ||  |      |   |   | |||| |                      
ACAAAAGGACAAGAGTTTCAGTGGCTCTGTTAAGTTGCCTCGCATCCCTCGTCCAAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCACGTTGAGGAGgtaaacaggcagttgatgatgcacttgaaaatgtacttatttagttgttgaacatgcttgcagtagtaaatctgcaaaaacactaatgcttcgagttact

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag-attgagcgccctc------tctcctttagttgccggattgaatcac--tggtccattgcttttttgcacag-----------------------
 |||||||||||||||||||| ||||| || |||||||| |||||  | || |||||||||| | | |||||||| |||||||| |||||||| |  |||||    |||   |    ||       ||| | | | | |   | |   |||   |  |    | |||  |||||                          
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcact-ggtccattgcttttttgcacag---------------------------------
 |||||||||||||||||||| ||||| || ||| |||| |||||  | || |||||||||| | | |||||||| |||||||| |||||||| |  ||||||    | |    ||    || |  |    |   ||     || |   |    |||| |   | ||                                   
ACAGAAGGACAAGCGTTTCAGTGGCTCCGTCAAGTTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtat--ctaatttgccctattcatcgaaactctttatgttgccatttaattaggtgctgtagggaacccccaagtttaagaaattaacctcattgttatctt

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcac-tggtccattgcttttttgcacag---------------------------------
 |||||||||||||||||||| ||||| || ||| ||||||| ||| | || ||||||||||   | || ||||| || ||||| ||||| || |  ||||||| | | |      |         |    |  |||| ||||   || | ||||| |||  |  | |                                  
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatt--tatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaa------gattgagcgccctctctccttt---agttgccggattgaat-cactggtccattgcttttttgcacag-----------------------
 ||||||||||||||||| || ||||| || ||| ||||||||||| | || ||||||||||   | || ||||| || ||||| || || || |  |||||||      |||  |     |   | | | |   || |     ||||  | || |  |  ||||||||   | || |                       
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacag-actgtgtttgcttcctttccatttata

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 5
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgcc------ggattgaatcactggt-ccattgcttttttgcacag-------------------------
 |||||||||||||||||||| || || |||||| |||| |||||  | || ||||||||||  || |||||||| |||||||| || || || |  |||||||   ||  |  | |  || | ||| | ||       | | ||||  ||  ||  |||||||  ||     |                          
CCAGAAGGACAAGCGTTTCAGTGGTTCTGTGAAGTTGCCCCACATCCCTCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCTCAACACGTGGAAGAGgtaattgtgctccacttggctgcattaatggcaataaaagaagtgaaagacaagtgtcattgctaattgaagaatatttttcaactatttttttgtttaa

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv08s0007g03340.t01 (Vitis vinifera), 5'ss of exon 3
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcct--ttagttgccg-gattgaatcactg---gtccattgcttttttgcacag--------------------------
 || |||||||||||||| || || || ||||||||||| |||||  | || || |||||||   | |||||||| |||||||| |||||||| |  |||||||  |   |      ||   ||    | |  | | ||   || || |     |  |||    |||  |  |                           
CCAAAAGGACAAGCGTTTTAGTGGGTCTGTGAAGCTGCCACACATCCCTCGTCCTAAGATGAAGATCTGCATGCTTGGTGATGCTCAGCATGTGGAAGAGgtaaattactgttttgacttatctaacaaataactgagaacaaaacaataaaaattgattttgatttctcctatcattttttaatccttgattttcctgt

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagatt---------gagcgccctctctcctt-tagttgccggatt----gaatcactggtccattgcttttttgcacag---------------------
 ||||| ||||| |||||||||||||| ||||||||||| |||||| | || || |||||||||||||||||||| || ||||| ||||| || |  ||||| | |||         ||      | |  | |  || |||    |||    || |  || |   | ||  |  || |  |                      
CCAGAAAGACAAACGTTTCAGCGGCTCTGTGAAGCTGCCACACATTCCTCGTCCTAAGATGAGAGTGTGCATGCTTGGAGATGCTCAGCACGTCGAGGAGgtcatattcgcacattggaataatttttgccttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaaccaacgttcatctgacaatag

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaaga--ttgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacag------------------------------------------
 ||||| |||||||||||||| || || ||||||||||| |||||| | || || |||||| | |||||||||||||| ||||| ||||| || |  ||||||     |  | | |      | |      ||  |    | ||   ||      |||    || | |||                                          
CCAGAAAGACAAGCGTTTCAGTGGTTCCGTGAAGCTGCCACACATTCCTCGCCCTAAGATGCGCGTGTGCATGCTCGGAGATGCCCAGCACGTTGAGGAGgtatttcctctaactcaactaatgccacccatgttgagaagcatt-ttgtcagcatgccacattacgcaggttgattacctcttatttattcgccccattattgcgtaacag

upper sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 5'ss of exon 2
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgcc--------ctctctcctttagttgccgg--------attgaatcactggtccattgcttttttgcacag-------------------------------------------------------------------------------------------------------------
 ||||| |||||||||||||| ||||| |||||||| || |||||| | || || ||||||||  | || ||||| || ||||| || ||| | |  |||||| | ||   | |          ||| ||  || ||||  ||        ||||||| |    |       |||| ||| | |                                                                                                             
CCAGAAAGACAAGCGTTTCAGTGGCTCCGTGAAGCTTCCCCACATTCCTCGTCCTAAGATGAGGATTTGTATGCTTGGAGATGCCCAACATATTGAAGAGgtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacag

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), 35 (downstream exon)
Score: 24

GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattga ... ttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG