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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaagaacttgttaatggagtgacggcttgttactccgtgctagtacag

Basic information

species Selaginella moellendorffii
transcript EFJ21207
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21207 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 7
CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaaga----acttgttaatggagtgacggcttgttact-ccgtgctagtacag----------------------------------------------
  | ||  |  | |||||  | || || || ||||| ||||| || ||  | || |||||||||||||| || ||||| || |||||||| ||||| ||||||| |    | ||  |  |  | ||       || | | || |     ||||                                               
AACTGGTTTAGCAGAAGTAAGGCGGTCAAGGAGGCTCACTGTTTCATTTATCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttcatttcctcttataatgttacaaagtaagtaccatttacctacaatacccaatatatatattatctatacaagttgattaccgctcactga

upper sequence: EFJ21207 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: AT2G42490.1 (Arabidopsis thaliana), 5'ss of exon 7
CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaagaacttgttaatggagtgacggcttgttactccgtgctagtacag-----------------------------------------------------
  | ||| |  | ||||| ||| |||| || || |||||||| ||||| || || || ||||| |||||||| ||||| || |||||||| ||||||||||| ||       ||   || |      || ||       ||   ||                                                        
AACAGGATTAGCCGAAGTGCGAAGATCTAGGAGACTAACTGTCTCTTTTCTATGTACTGTTGCCAACTACGAGTATGGGTTTTACTGGCACTTCTACCAGgttagtgg--aatacgtgattcttcatttcttgagtaaagcagatattagtcatatttgcatctaatttctatagggaagacaaatgatgtgtctccgcatg

upper sequence: EFJ21207 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 7
CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaag----aacttgttaatggagtgacgg---cttgttactccgtgctagtacag--------------------------------------------
  | || ||  | || ||||| || || ||||||||||| ||||||||  | ||||| ||||||||||| || || || |||| ||||||||| || |||| |||    |  |   | ||   ||  | |    |  ||  ||    || || | |                                            
AACAGGTCTAGCAGAGGTTCGTCGTTCTAGAAGGCTAACAGTGTCTTTTGTATGCACTGTTGCAAACTATGAGTACGGATTCTTCTGGCATTTTTATCAGgcaagttaaatttcccttattttgtttcaggatttaatttttcttctcttgtgcggattggcaagataaattattctcatctcaaagctatcactttctt

upper sequence: EFJ21207 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: PP1S363_39V6.1 (Physcomitrella patens), 5'ss of exon 6
CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaag-------aacttgttaatggagtgacggcttgt-tactccgtgct-agtacag------------------------------------------
  | ||     | |||   || || |||||  |  ||||||| |||||| ||||||| ||||| |||||||| || || || |||||||||||||| |||||  |       ||||  ||| | ||   |   | ||| |||   |  || | || |                                           
AACTGGTTCTACAGAAAGACGTCGGTCGAGGCGTTTAACTGTTTCTTTCTTTTGCACTGTTGCCAACTACGAGTACGGGTTTTACTGGCATTTCTATCAGgtttggtgctgaaactgcttacttgatgcatatcctgtctacaaagaactgactagaagatcttggtgttctgtctccacatgcaacacacaacagtagt

upper sequence: EFJ21207 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: PP1S9_129V6.1 (Physcomitrella patens), 5'ss of exon 8
CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaagaacttgttaatggagtgacggcttgttactccgtgctagtacag-----------
  | ||     | |||   || || ||  |  |  |  | || || ||  | ||||| ||||| ||||| || ||||| ||||||||||||||||| |||||   |  || ||  ||   |   |  |  ||  || |   ||  | ||           
AACTGGTTCTGCAGAAAGCCGTCGGTCTCGGCGATTGTCCGTTTCGTTTTTCTGCACTGTTGCCAACTATGAGTATGGTTTCTACTGGCATTTCTATCAGgttttattttcttt-tgccctcctgtatacttgttctgc-ttacaaaaggatgtttacag

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|169069290|gb|FE480049.1|FE480049
EST:     TTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAG                         GATGGAAAAATAGAGGCTGAGGTGAAGCTCACGGGGATTCTCAGCCTGGGA
genomic: TTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaagaactt ... gctagtacagGATGGAAAAATAGAGGCTGAGGTGAAGCTCACGGGGATTCTCAGCCTGGGA
EST: gi|169092718|gb|FE493686.1|FE493686
EST:     TTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAG                         GATGGAAAAATAGAGGCTGAGGTGAAGCTCACGGGGATTCTCAGCCTGGGA
genomic: TTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaagaactt ... gctagtacagGATGGAAAAATAGAGGCTGAGGTGAAGCTCACGGGGATTCTCAGCCTGGGA

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: 26 (upstream exon), 33 (downstream exon)
Score: 4

CTCGGGACTCTCTGAAGTTCGACGATCGAGAAGGCTAACTGTGTCTTTCCTTTGCACAGTTGCAAACTACGAATATGGCTTCTACTGGCATTTCTACCAGgtaagaactt ... gctagtacagGATGGAAAAATAGAGGCTGAGGTGAAGCTCACGGGGATTCTCAGCCTGGGAGCACTTCGTGCTGGAGAAATCAGGAAATACGGGACTGTTATAGCTCCTG




<











<


<