Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttcttcctcgtctagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG

Basic information

species Selaginella moellendorffii
transcript EFJ37626
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
--------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
                                                                                  | ||||| ||    ||| |    || || ||   | ||  | || ||   |||| || || || ||||||| ||| | | | ||||| |||||||| ||| |||| || || |||||||||||||||||||| ||||| |||||||| || |
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaaca-atctttattttatgtggtcttactc-tagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG

upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------gttcgttcttcctcgtc-tagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
                                                  || | | ||      |  |     |  ||| |   | | | |  ||   || |||||||||| || ||||||| ||| | | | |||||||| ||||| |||||||| ||||| || || ||||||||||| || ||||| || || || || |
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaata-tgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 8
----------------------------------------gttcgttcttcctcgtctag-actgta--ttttgatcgaaagt--atttttgct-tgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
                                         || ||   |||    |||| |||  |  ||   |   || |   || | || | || |||| |||||||||||||||| |||||   | ||||| |||||||| ||| ||||||| || || || || |||||||| ||||| |||||||| || ||||
aataagaaagggattctagcccccctccaatccccttcggttttgtggctcccaaactagcactaaaggttccaaaataacgccgatctatgttgtgtagATCCACTCGAGGAAAATGAATGTGAATCCAGATGTCAACTTTGAAGAGTTGGCGCGTTCAACCGATGATTTCAATGGCGCTCAGCTAAAGGCTGTTTGCG

upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtatt-ttgatcg----aaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
                                                                                                                      | |    ||    |   ||  | | || |  |||     || | | |||  | | |||||||| || |||||||||| |||  |    ||||| |||||||||||| |||| || |||||||||||||| || || || ||| ||||||| || ||| 
gttcggataaacaatagcgcttggtagactttgaagtttgcataatcctgtacccctaacctaaccatgttttcacctattgttttactgtttgatccttctataattataccacctatacagatttttatgagcaggatatcttatcaatcactgtaatgaactttcacctccagATTCATTCAAGGAAAATGAATGTACGGGGTGATGTCAACTTTGAGGAGTTGGCCCGTTCCACGGACGACTTTAACGGAGCCCAATTAAAGGCTGTATGCA

upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
                                                                                                         | | || | | || |  | | |   |   |     | | |||     ||||||||| ||||||||||||| | | ||  | ||||| |||||||||||| |||| ||||| || || ||||| || || |||||| | ||||| |||||  
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA

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|169044441|gb|FE450558.1|FE450558
EST:     AGATCGAATTTCCTCATCCCACCGAGGATGCCCGAGCGAGAATCTTACAA                         ATTCACTCGAGGAAAATGACT
genomic: AGATCGAATTTCCTCATCCCACCGAGGATGCCCGAGCGAGAATCTTACAAgttcgttctt ... ttgcttgcagATTCACTCGAGGAAAATGACT




















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: 19

AGCAGATATTCTAGACCCGGCTCTGATGCGATCTGGCCGTCTGGACAGGAAGATCGAATTTCCTCATCCCACCGAGGATGCCCGAGCGAGAATCTTACAAgttcgttctt ... ttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcgttcttcctcgtctagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
                           ttttgat  putative branch site (score: 19)
                                          tttttgctt  putative PPT
                                    aaagtattttt  TA-rich tract