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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgtcgtctgtctttgtacaagtttaaactcctgcttgtggtatcttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA

Basic information

species Selaginella moellendorffii
transcript EFJ37593
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------------------------------------------------------------------------gtttgttgtcgtctgtctttgtacaagtttaaactcctgcttgtggtatcttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA
                                                                                                                       | |   |   |     |||  |  |     || | |||||       ||   || ||||| || ||||| ||  ||||||| |||||||||||||| || ||  |||||||  |||| || |||||| | ||||| ||||||| |||||| |||||||
gtaatctttgttcgaaccaacattactttttatgtcttttgctggacagtttttgtgctataatttactttgctctgtggtggttttgacaaagtggtagactttattttctttaaaactctcgaggaattgaaatttacaagaaaactaagttctgctgcaaccttccatgttcagATCCATTGGTTCTCCATCTTCAATTCGTTCATGATGGTTATTTTCTTGACTGGATTGGTATCAATGATATTGATGAGGACGCTGAGAAATGATTATGCGA

upper sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------gtttgttgtcgtctgtctttgtacaagttt-------aaactcctgc----ttgtggtatcttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA
                                                            ||  |    ||  ||| |   | |  | |       | | |  |||    ||||  | | ||     ||||||| ||||| ||  | || ||||| |||||||||||||| || || |||||  ||||||| |||||| | ||| |||| |||| |||||||||||| |
gtacagctttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatagctctgccactgagaattttgctcctttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGTTTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------gtttgttgtcgtctgtctttgtacaagtttaaactcctgctt-gtggtatcttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA
                                                                     ||| ||  |    | ||| |||    |  ||   | || ||| ||  | | ||     ||||||| ||||| ||  | || ||||| |||||||||||||| || || |||||  ||||||| |||||| | ||| |||| |||| |||||||||||| |
gtacaactttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatatctctgtcactgagtattttgctcctttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------------------------------------------------------------gtttgtt-gtcgtctgtctttgtacaagtttaaactcctgcttg-tggtatcttcg--tgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA
                                                                                                                                    |   ||| | ||| ||    |||     ||     |  || | | |||   |  ||    ||||| || ||||| ||  |||||||||||||||||||||| ||||||||||| || ||||| || ||||| || ||| | || ||    || || |||||||
gtgggtgtgaggagggagcggagggctgagttgcaagatttgtgtagcgagtgtgggtggagacgggagcttgaagctacatgcgagttagtggtgtgttggaggttcatgggatggtgaatgggacgagtcgcgagtttgacgtgtgggggtgtttggtttgtggttgatgttgggtggcggccgcgatgacagATACATTGGTTCTCTATCTTCAACTCGTTCATGATGGTGATATTTCTGACGGGGCTGGTATCGATGATTCTGATGCGCACCCTCCGCAACGATTATGCGA

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|169044497|gb|FE451095.1|FE451095
EST:     TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAG                         ATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
genomic: TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAGgtttgttgtc ... cttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
EST: gi|169087209|gb|FE493117.1|FE493117
EST:     TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAG                         ATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
genomic: TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAGgtttgttgtc ... cttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
EST: gi|169088032|gb|FE492595.1|FE492595
EST:     TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAG                         ATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
genomic: TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAGgtttgttgtc ... cttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
EST: gi|169095561|gb|FE498837.1|FE498837
EST:     TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAG                         ATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT
genomic: TCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAGgtttgttgtc ... cttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACT

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: 28 (upstream exon), 34 (downstream exon)
Score: 10

ATCCCTGGAGTTTACATACTCCGTGAAATGGATCGAGACAAACACGAGTTTCCACAAGAGATTTGATGCCTACCTGGACTATCCATTCTTTGAGCATCAGgtttgttgtc ... cttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtcgtctgtctttgtacaagtttaaactcctgcttgtggtatcttcgtgcagATTCACTGGTTTTCGCTCTTCAACTCGTTCATGATGGTCATATTTCTGACTGGCCTGGTGTCTATGATACTCATGAGAACGCTGAAAAATGACTATGCGA
                                          tatcttc  CT-rich tract
                    aagtttaaa  TA-rich tract