Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgctcgtgagttctttctttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

Basic information

species Selaginella moellendorffii
transcript EFJ32796
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os08g35440.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------gtatgatgct-cgtga--gttctttctttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                                         |  |||  | | | |  ||     | ||   | |  | |      | ||   ||||    |  ||||||||||||| ||||| |||||||| |||||  |||| || || ||||| ||||| ||||| || ||||| || || |||||| ||||  | |||||  |||
gcaagccgccatcgccatcgccacctcctcctcccgtgcgttgcgattttgcataatcgtctcaaccttgaagctcttcttgcgttcttgggggcaaatggacgaacagGTGGTGGAGGACGGCTACGAGTTCTTCGCGGACAGGCAGCTGGTGACCATATTCTCGGCGCCGAACTACTGCGGCGAGTTCAACAACGCCGGCGCGCTGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G112240_T01 (Zea mays), 3'ss of exon 2
-----------------------------gtatgatgctcgtgagttctttctttattgttgctttgagccccatgtctgcaataacaataa-cagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                              ||| |   |    | | |    | |||   |  ||| |        | |||| |    | |  ||||| || ||||| ||||||||||||||||| | | | ||||| || || |||||||| || || ||||| ||||| || ||||||||  | || || ||||
gttgttgtgttcttaaagatgtgacctacttattaccttataaactacaaagtgtatcaatagttt-acttatgcttttgcattgttgaaattcagGTTGTCGAAGATGGATACGAGTTTTTCGCTAGCCGTCAACTCGTAACAATATTTTCAGCCCCTAACTACTGTGGAGAATTCGACAACGCTGGTGCCATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA03G41200.1 (Glycine max), 3'ss of exon 2
------------------------------gtatgatg---ctcg-tgagttctttctttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                              | ||  |    |||| | |  | |    ||     |   |||       | |  |   |     || ||||| |||||||| ||||||||||| || || ||  |||||||||| || |||||||| ||||| || |||||||||||||| |||||| | || |||||||
tactgtacatgcctttatgtttagatcgggggatagtaggcctcgatcaactatgctattgaaagtaaattgttttttgttttcggcctttttttaccagGTTGTGGAAGATGGATACGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAGTTTGACAATGCTGGTGCTATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G36510.1 (Glycine max), 3'ss of exon 2
---------------------------------gtatgatgctcgtgagttctttct-ttattgttgctttgagccccatgtctgcaataacaat--aacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                                 | ||  |     | | | |  |||  ||||     ||| |     ||   ||   | ||  |  |||||||||||||||| || || ||||| || || ||| | || ||||| || |||||||| ||||| || |||||||| ||||| |||||| | ||||||||||
attctttacattcctgcatttatttacattgaaggatagtatctatcaatccgctctgctatta--aatttaaattggattaatgttttgacttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
--------------------gtatgatgctcgtgagttctttc----------tttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                     | ||| | | | |  | |  |           || |    |    | | |  | ||| ||   |  |  |   |||| || ||||| ||||| |||||||| ||||| |||||||||||||| || ||||| ||||| ||||| ||||| || || |||||| | || || ||||
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgtttt--cttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
------------------------------gtatgatgctcgtga--gttctttcttta--ttgttgc-tttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                               ||| | |||  |||   ||| |||||||  ||  ||| ||| |     ||   ||          | ||||||||||| || || |||||||| || || ||| | || ||||| || |||||||| ||||| || |||||||| ||||| |||||| | ||||||||||
gaggctaaacttctccctttcaaatgccacttatta-gcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttttgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
----------------------------gtatgatgctcgtgagt-tctttctttattgttgctttgagccccatgtctgcaataaca-----ataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                             |  |  | | ||  || ||  ||     || |  |   |      | | |    |  |       || ||||| |||||||| ||||| ||||| || || ||  |||||||||| || |||||||| ||||| || ||||||||||| || |||||| | || |||||||
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G33040.1 (Glycine max), 3'ss of exon 2
---gtatgatgctcgtgagttctttctttattgttgctttgagcc--------ccatgtc-----tgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
     ||  | ||  | | |  | |  || |  | |||  ||  |        | ||||      |  | |     | |||||| || ||||||||||| || || || || |||||||||||||| || || || |||||||| || || ||||| ||||| |||||| | || |||||||
gtttcatagtccttttaaata-tgtgattgtaatggctaggaatcaaaatgtacaatgttctgattatattgggtgttacagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA02G00850.1 (Glycine max), 3'ss of exon 2
---------------gtatgatgctcgtgagttctttcttt------attgttgctttgagc--cccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                ||||| | | | | || |  |  ||       ||   |  |||     ||    | ||   |  |  |   |||| || ||||| ||||| || |||||  |||| |||||||||||||| || ||||| ||||| ||||| ||||| || || |||||| | || || ||||
gttttatatgcatttctatgaagtttgagtgtgcaattgttggaagagttcaagtattgcataacctgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT5G59160.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtatgatgctcgtgagttcttt---ctttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                           |||  | ||   ||  ||      |||   |     | | |      ||| |    |     ||| |||| || || || ||||| |||||||||||| | ||||| ||||| ||||||||||| || |||||||| ||||| || || |||||| | || |||||||
gttcgtcgtctacacactgttcgtttctattttactaaagatgtcacggaacttctataaaaatataactgttgtgtttttctttttc-taaaagGTTGTAGAGGATGGATATGAGTTTTTCGCCGATAGACAGCTTGTTACGATATTTTCTGCTCCCAACTACTGTGGTGAATTTGACAATGCTGGTGCTATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------gtatgatgctcgtgagttctttctttattgttgctttgagccccatgtc-tgcaataacaata-----acagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                                                                                                         |  | || |  ||      |   |  || || |    ||||   | |     ||  | | |       ||||| || ||||| ||||||||||| || || || |||||||| ||||| ||||| || |||||||| || ||||| ||||| |||||| | || ||  |||
gtaaagctaaaatttattccttgagttctctcttttgatttctctggattggtttgttcttctctgtgactgttctctgaattcagagggttaagaaatcataactcagttgttaatgcaaggatctgtagttttttcaccaagccaagttttacttaactatactgttcctgcagGTTGTAGAAGATGGATACGAGTTCTTTGCAAAGAGACAACTAGTGACAATATTCTCTGCACCCAATTACTGTGGCGAGTTTGACAATGCTGGTGCATTGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv05s0049g00890.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtatgatgctcgtgagttctttcttta-------ttgttgctttgagccccatgtctgcaataaca-ata----------acagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
           || | |   |  ||  || ||| |||        ||    || | || |   | |||   |  ||| ||            ||||| |||||||| |||||||||||||| || || ||||||||||| || |||||||| ||||| || || ||||| ||||| || ||| | || || ||||
gtttcagctctgttttagctttttgcattttttttttggtcacctttaaacctctcaggcatttttctcttactacatatttccttgttgtgcagGTTGTGGAAGATGGATACGAGTTTTTTGCTAATAGACAACTTGTAACCATATTTTCAGCACCTAATTACTGTGGTGAGTTTGATAATGCGGGTGCCATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------gtatgatgctcgtgagtt----ctttctttattgttgctttgagccccatgtctgcaata-acaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                              | ||||  |  |  |||    ||    ||| |  ||  ||| |       |||     |   | |  ||||| |||||||| || || |||||||| || || || || || ||||| ||||| |||||||| || || ||||| |||||||||||| | || || ||||
acatccctgtgtgtttattatctgtggttatgtgattttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA

upper sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
-gtat-gatgctcgtgagttctttctttattgttgctttgagccccatgtctgcaataacaataac-agGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
  ||| |    ||     || || | || ||  |   |   ||  |        |    |  |  | |||| |||||||| ||||| || || || ||  ||||||| ||||| || |||||||| || |||||||||||||| || || || ||| | || || ||||
gttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

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: 33 (upstream exon), 34 (downstream exon)
Score: 7

GGGTCAGAATGATCGAGGTGTCTCATTTACATTTGGTAGCAACGCGGTTGCGGAGTTTCTTCAAAAACAGGACCTCGATCTCATTTGTCGAGCTCATCAGgtatgatgct ... acaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagttctttctttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
                                        caataac  putative branch site (score: 7)
                                         aataacaataa  TA-rich tract