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

gtaagtcttccccttgtttataagctaagcgtcgtaaacgatttaaaaaattgcctctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTTCTGAGCGATCTCTTCTGGGTTGGAATGTTTT

Basic information

species Selaginella moellendorffii
transcript EFJ38162
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: AT5G46110.3 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------------------------------------------------------gtaa-gtcttccccttgtttataagctaagcgtcgtaaacgatttaaaaaattgcctctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTTCTGAGCGATCTCTTCTGGGTTGGAATGTTTT
                                                                             |||| |||||    ||  |||| |  || |  |  |        | |||| |||    |     || | || ||||| || ||| |  | || || || || || || ||||| ||||||||||||   || ||  |    |||||||||||||||||||||||||
gcactcttcgtctgcattcctcctgccatcatcgttaagtcactttcattatttctcactagttacgtatgaaagaagtaatgtctttttttttgttattaattagggtttctgg------ttaaaatttgttctt-----agGTTGAAGGTCCTAAACTACTTAACCATGGTTTCGCCGACGCGATTGCTAAAGTTGGAATGACTAAATTCATCTCTGATCTCTTCTGGGTTGGAATGTTTT

upper sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------gtaa-gtcttccccttgtttataagctaagcgtcgtaaacgatttaaaaaattgcctctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTTCTGAGCGATCTCTTCTGGGTTGGAATGTTTT
                                            |||| |||||    ||  |||| |  || |  |  |        | |||| |||    |     || | || ||||| || ||| |  | || || || || || || ||||| ||||||||||||   || ||  |    |||||||||||||||||||||||||
gttaagtcactttcattatttctcactagttacgtatgaaagaagtaatgtctttttttttgttattaattagggtttctgg------ttaaaatttgttctt-----agGTTGAAGGTCCTAAACTACTTAACCATGGTTTCGCCGACGCGATTGCTAAAGTTGGAATGACTAAATTCATCTCTGATCTCTTCTGGGTTGGAATGTTTT
















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|169057525|gb|FE464477.1|FE464477
EST:     CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTG                         ATGGAGGGTCCCAAGCTATTTGCA-CACGGGTTTGCAGATGCCATTGCCAA
genomic: CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATT-GCAACACGGGTTTGCAGATGCCATTGCCAA
EST: gi|169055191|gb|FE462404.1|FE462404
EST:     CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTG                         ATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
genomic: CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
EST: gi|169098868|gb|FE502265.1|FE502265
EST:     CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTG                         ATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
genomic: CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
EST: gi|169086705|gb|FE494342.1|FE494342
EST:     CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTG                         ATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
genomic: CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
EST: gi|169104796|gb|FE505391.1|FE505391
EST:     CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTG                         ATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
genomic: CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
EST: gi|169041079|gb|FE450366.1|FE450366
EST:     CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTG                         ATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA
genomic: CCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAA

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: 37

ACCGGAATGGACAGTACAAACGTTTATGCCTACATTTCAATCCTGTCTCTGCTCTTCTGCATTCCTCCAGCAGTGGTGgtaagtcttc ... tctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTTCTGAGCGATCTCTTCTGGGTTGGAATGTTTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttgtttataagctaagcgtcgtaaacgatttaaaaaattgcctctcacacagATGGAGGGTCCCAAGCTATTGCAACACGGGTTTGCAGATGCCATTGCCAAAGTTGGAATGGTGAAGTTTCTGAGCGATCTCTTCTGGGTTGGAATGTTTT
                                            ctctcac  putative branch site (score: 37)
                                        ttgcctctc  CT-rich tract
                        taaacgatttaaaaaa  TA-rich tract