Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgtatcgtatcgatcttaagttggctgacgagaagatgaaaaaatttgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG

Basic information

species Selaginella moellendorffii
transcript EFJ22847
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os06g15480.2 (Oryza sativa), 3'ss of exon 7
--------------------------------gtaagctgtatcgtatcgatcttaagttggctgacgagaagatgaaaaaatttgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                                 | |||   |    |   |||| ||| |  |          ||     |   |||| |||  ||   | |||||    | || || ||||| || || || |||||||||||||| || |||||||| ||||| || ||||||||||||||||||||  |||||||||
gttttgacacgatcgagtgatcacccacccaattcagcaacaagcaaagaatctgaagctaccattgaccgccattgttgatgatgttgtttg-tgcagGTTCTTGCCAGC-CATCTTGAGCCGCTGACGGATCAGCAGCTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCGCAGG

upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os10g41640.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtaagctgtatcgtatc--gatcttaagttggctg--acgagaagatgaaaaaatttgt-ttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                               ||||   | |  | |||   | ||    ||| |||  |       ||||  |   |  | || ||| ||   |  |||||   | || || ||||| || ||  | |||||| ||||||| || |||||||| ||||| || ||||||||||||||||||||  |||| ||||
gtttgacacgagtgatcacccacccaattcagtaacaagcaaagaatctgaagctaccattgactgctattgttgaatgatgatgatgatgttgtttgtgcagGTACTTGAGAGC-CATCTTGAGCCGCTGACGAATCAGCAGTTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCACAGG

upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os01g65970.1 (Oryza sativa), 3'ss of exon 1
-------------------------gtaagctgtatcgtatc--gatcttaagttggctgacg-----agaagatgaaaaaatttgtttt-tttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                         ||||   | |  | |||   | ||    ||| |||          | |||||  |   |  | || ||| ||   | ||||||   | || || ||||| || || || |||  | | ||||| || |||||||| ||||| ||||||||||||| |||||||||  |||||||||
cacgagtgatcacccactcaattcagtaacaagcaaagaatctgaagctaccattgactgctattgttgaatgatgatgatgatgatgttgtttgtgcagGTTCTTGAGAGC-CATCTTGAGCCACTGACGGATCAGTTGTTTATGGGCATCTGCAACCTACAGCAGTCCTCGCAGCAGGTCGAGGACGCGCTGTCGCAGG

upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os05g37170.4 (Oryza sativa), 3'ss of exon 11
--------------------------------------gtaagctgtatcgtatcgatcttaag--ttggctgacgagaagatgaa--aaaatttgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                                      | | | | |||     |   || ||   |||||           |     |  |||||  ||||||    ||||  |||| || ||||| || || || || |||||||||||||||||||| |||| ||| ||||| || ||| ||||| ||||||| ||  |  ||||||
gtagacacacaacataattttttttttcagtaagacacgcacgat-tattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttc-accagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG

upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 8
----------------------gtaagctgta--tcgtatcgatcttaagttg-gctgacgagaagatgaaaaaatttgtttttttctgttagATCTTGATTCCA-------CAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                       ||   | ||  ||||| |  ||    | ||      |   ||||||||  | |   |    |||||  | ||      |||        ||||| ||||| || || ||||||||  |||||||| | | ||| |||||||||||||| |||||||| ||||| || ||||| || |
tctttagccgggcgtggtttttttattttatagttcgtaccattcaatggctgtatctgcttcaagatgaactattccttacacttctgcaaaattgcagCTCCTTGTGAATCAGCTTGAGCCTCTAACTGAGCAGCAATTGATGGGGCTATCCAATCTCCAGCAATCCTCCCAGCAGGCTGAGGATGCATTGTCACAAG

upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AC232238.2_FGT004 (Zea mays), 3'ss of exon 9
-----------gtaagctgtatcgtatc-gatcttaagttggctgacgagaagatgaaaaaatttgtttttttctgt------tagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
           ||  ||   | |   || ||   | ||  |||   |  | |  |||     ||| | ||||||| |       || || |||| || |||||||| || || || |||||||||||| ||||||| |||| ||| ||||| || ||| ||||||| ||||| ||  |  | ||||
gtcgtccgtccgtgcgccccacccagtctgagtctgaggcggcgcgcc-gtacttgagcctctttctctttttctttgccatgcagGTCCTGATACCGCAGCTGGACCCGCTGACGGAGCAGCAGCTGCTGGGGATCTGCAGCCTGCAGCAGTCGTCGGAGCAGGCGGAGGAGGCGCTCGCCCAGG

upper sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA15G37220.1 (Glycine max), 3'ss of exon 6
----------------------------gtaagctgtatcgtatcgatct-taagttggctgacgagaagatgaaaaa-atttgtttttttctgtt--agATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
                             |  | | | | |  ||  | | ||| ||   ||||    |  | |      |   |||  ||   ||  || |  || ||   ||  ||||||| ||||| ||||||||||||||||| |||  |||| | ||||||||||| || || || || || || || || ||||
ttcataattgtggctactgaggttttatttcggatatgtggagtcattttataatttccttgactttgactttagtcctgtgaatttggttgcattgcagCTGCTGGTTAGTCAATTGGAGCCTCTCACAGAGCAGCAGCTGATGGGTATTACCAACTTGCAGCAATCCTCCCAACAAGCAGAAGATGCATTATCTCAGG

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: 30 (upstream exon), 35 (downstream exon)
Score: 14

CAAGGCCGACGTCTTCCACCTCGTCTCCGGGATGTGGAAGTCTCCCGCCGAGCGCTGCTTCATGTGGATGGGAGGATTCAGACCCTCGGAGCTTCTCAAGgtaagctgta ... tttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcgatcttaagttggctgacgagaagatgaaaaaatttgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG
               ggctgac  putative branch site (score: 14)
                                     tttgtttttttctgtt  putative PPT
                         aagatgaaaaaatttg  TA-rich tract