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

gtatgagattacgagtttcttctctctcactttggcaaattggaaattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG

Basic information

species Selaginella moellendorffii
transcript EFJ30542
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------gtatgagattacgagttt--cttctctctcactttggcaaa-------ttggaaattttca--agGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG
                                    | | || | | | ||||   || |   ||| ||     |         | ||| || | |  ||||||| ||||| || |||||| |||| |||||||||||||| |||||||| || || ||  ||||| | ||
ctccaccactccttacaaaatatttagcttctggaatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG
















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|169047767|gb|FE454623.1|FE454623
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
EST: gi|169042136|gb|FE454179.1|FE454179
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
EST: gi|70669602|gb|DN838179.1|DN838179
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
EST: gi|169074100|gb|FE481747.1|FE481747
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
EST: gi|169074099|gb|FE481746.1|FE481746
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
EST: gi|169054140|gb|FE462375.1|FE462375
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
EST: gi|169036632|gb|FE446556.1|FE446556
EST:     CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAG                         GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC
genomic: CGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGC

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), 33 (downstream exon)
Score: 39

GCTTGCAAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagatt ... aattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgagattacgagtttcttctctctcactttggcaaattggaaattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG
                        ctctcac  putative branch site (score: 39)
                                               ttttc  putative PPT
                                     aaattggaaatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagattacgagtttcttctctctcactttggcaaattggaaattttcaagGCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC