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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttcttttgtttattgtcttgaaaagttagtgctcatcgtgagtgcttttcttttacag

Basic information

species Selaginella moellendorffii
transcript EFJ11220
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g26850.2 (Oryza sativa), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgta---------ctcacgacttcttttgttt-attgtcttgaaaagttagtgctcatcgtgagtgctt-------ttcttttacag--------------
|||||||||||| |||||||||||||||||||||||||||  ||  ||  | || |||||||| || ||||| |||||||| || |||||||||||||||||          ||| |  | | | |  |   ||| | ||  | |  |   |||  | | |   || |       | ||| ||| |              
GGAGACCACCACCGGTGTCAAGAGGCTCTACCAGATGCAGGAGACCGGCGCCCTCCTCTTCCCCGCCATCAACGTCAACGACTCCGTCACCAAGAGCAAGgtgaagcatcccctccctccctttctaatcccattatatttcagatctgaagctgtttgcgttagcctagcctgctgcttgtactgttcttaccttagta

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G015295_T01 (Zea mays), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgt-actcacgacttcttttgttt------attgtcttgaaaagtta--gtgctcatcgtgagtgcttttcttttacag----------------------
|||||||||||| |||||||||||||||||||||||||||  ||  ||  | || |||||||| || || || ||||||||||| ||||||||||||||||| | ||  |  | | ||| |||      |||  |||  | |  |   || ||  | ||| |    |   |  | ||                       
GGAGACCACCACGGGTGTCAAGAGGCTCTACCAGATGCAGGAGACCGGCGCCCTCCTCTTCCCTGCCATTAACGTCAACGATTCCGTCACCAAGAGCAAGgtgattcttgcttgcctttctttggatccatttcctttcagatctgacgttcttgttgtgtggatctagatcctgcatgactagcagtgtgagatttact

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G11480.1 (Glycine max), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttctttt----gtttattgtcttg--------aaaagttagtgctcatcgtgagtgcttttcttttacag-------------------
||| ||||||||||| || ||||||||||| ||||||||| |||||||  | || |||||||| ||||| |||||||| || || |||||||||||||||||| |  |   || |        | || ||||||         ||||  |||   | |    |  |   ||  ||||  |                    
GGAAACCACCACTGGAGTTAAGAGGCTCTATCAGATGCAGGCGAATGGGACTCTTCTCTTCCCTGCTATTAATGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtctctttttcccccagatctagtgtcttttttgtgttaaaatgtaggattgagttcggatctgttgtttttggatgggttttgtgccattggtg

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA11G36620.1 (Glycine max), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga--cttcttttgtttattgtcttg---aaaagttagtgctcatcgtgagtgctt------ttcttttacag
 || |||||||| ||||||||||||||||||||||||||| | ||||| || ||  | ||||| || ||||| ||||| || || |||||||||||||||||||  || |  | | |||||| | ||   |||       || |  |         |||| ||       | | || |||
AGAAACCACCACCGGTGTCAAGAGGCTCTACCAGATGCAGGCCAATGGCTCCCTCTTGTTCCCTGCCATCAACGTCAATGACTCGGTCACCAAGAGCAAGgtacgtaccatacattttttgtctgtttgtttgtctgtcggtgaaagaaatataaaagtgtttgatgcaatttgttgcag

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA05G28480.1 (Glycine max), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtac--tcacgacttcttttg-----------tttattgtcttgaaaagttagtgctcatcgtgag-tgcttttcttttacag-----------------
||| |||||||||||||| |||||||| || ||||||||| |||||||  | || |||||||| ||||| |||||||| || || || |||||||||||||||   || |  |||||               |||  | | || ||| ||  ||     |   ||  || | |||||  |  |                 
GGAAACCACCACTGGTGTTAAGAGGCTATATCAGATGCAGGCGAATGGGACTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctcttcttctcccagatctggtgctttttatatgtttaaatgtaggtttgagttcagatctgttgttcttggatgggttttgtggcgttggtg

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT4G13940.1 (Arabidopsis thaliana), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttcttttgtttattgtcttgaaaagttag---tgctca-tcgtgagtgcttttcttttacag---------------------------
||| || ||||||||||| |||||||| ||||||||||||   |||||| | ||  | ||||| || || || || ||||| || |||||||||||||||||| | |        ||||||| ||  || |  | | ||    ||||   || | ||  || |  ||||  |                            
GGAAACTACCACTGGTGTTAAGAGGCTTTACCAGATGCAGCAAAATGGAACTCTTTTGTTCCCTGCCATTAACGTTAACGACTCTGTCACCAAGAGCAAGgtattgatcttcagatttgtttctttactagtgatgataaatctgctaggtctttagctctgtagtttttgatgcgataggcttaacaacaacataatca

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttcttttgtttattgtcttgaaaa-gtta-gtgctcatcgtgagtgcttttcttttacag--------------------------------
 ||||| ||||| ||||| |||||||| |||||||||||| | |||||| | ||  | ||  | |||||||||||||||||||| || ||||||||||||||| |   ||  |   || || | | | || |    ||||  | || |   |  ||||| || ||| | |                                 
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatg--gatctagatttttcactctttttagctcgttatatactgaatttt-gtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg

upper sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0029g00330.t01 (Vitis vinifera), 5'ss of exon 1
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttct------tttgtttattgtcttgaaaagttagtgctcatcgtg-agtgcttttcttttacag---------------------------------------------------------------------------
|||||||||||| ||||| |||||||| |||||||||||  | || ||  |  |||| ||||| ||||| |||||||| || || |||||||||||||||||| || | |  |||      ||||   ||||| || ||   ||    |   | ||   |||  | |  |||  |                                                                            
GGAGACCACCACCGGTGTTAAGAGGCTTTACCAGATGCAAGCTAACGGCACTTTGCTTTTCCCTGCTATTAATGTCAATGACTCTGTCACCAAGAGCAAGgtattctccagatctgtgatatttgggaattgttttcaacgattcaaccaatttgtttggtggatctagtttggattactagaagagtcgtaattttgtgttttgttttgttttgtttttcttaacaattttctgttctggatgcaaacag

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|169102874|gb|FE505239.1|FE505239
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169079936|gb|FE487874.1|FE487874
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169069332|gb|FE478830.1|FE478830
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169045949|gb|FE453105.1|FE453105
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169033067|gb|FE441401.1|FE441401
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTANCG-CTGCCGACACTCTCTCCCTGATGGACTCATGCG
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTA-CGGCTGCCGACACTCTCTCCCTGATGGACTCATGCG
EST: gi|169034478|gb|FE444551.1|FE444551
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169074158|gb|FE482390.1|FE482390
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169078937|gb|FE486589.1|FE486589
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169081968|gb|FE487477.1|FE487477
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169116228|gb|FE517175.1|FE517175
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCG
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACC-TTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCG
EST: gi|169025864|gb|FE433163.1|FE433163
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169025971|gb|FE432906.1|FE432906
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
EST: gi|169069671|gb|FE477024.1|FE477024
EST:     CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAG                         TTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA
genomic: CGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGA

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: 67

GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacga ... tcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGAGCAACTGATGTGATGATCGCTGGGAAGGTCGCAGTCGTCGCTGGATACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttcttttgtttattgtcttgaaaagttagtgctcatcgtgagtgcttttcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG