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

gtaccacaacattcttttgctcgtttttcttatcagccttgtttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG

Basic information

species Selaginella moellendorffii
transcript EFJ17401
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 3
------------gtaccacaacat----tcttttgctcgtttttcttatcagccttgtttttctttttcgtttc-tcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
             | |  |||  |    | |||  ||| |     | ||||   |  ||    | || | |  | | ||||||||||||||| ||| | |||||||| ||||| || ||||| ||||||||||| || ||||||||                                   
gtaaatatacaaatgcagcaatgtagtgtgtttacctcatgaacttgatcaatttgcttacaatgttgcttgccgttgcagATGTGGATTGCCAAGGCTGAGTACGACGAGTCTGGCCCATCCATTGTGCACAGGAAATGCTTCTAATTCTTCGGACCCAAGAATGCTAAGCCAAGAGGAG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 4
--------------------------------------------gtaccacaacattc-------ttttgctcgtttttcttatcagccttgt-ttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                             ||   |||| ||        |   |   | | ||  |   |      |  | || | ||  | |    |||||||||||  ||||| | |||||||||||||| || ||| ||||||| ||| | |||||||||||                                   
gttaaaaccttataacacttgttattttccagttgctatggcaaatattccaacctttcggtagttccagtaagctcttggttctaaaaacatgctctcgtatttatatgctacagATGTGGATCTCAAAGGCTGAGTACGATGAGTCAGGACCAGCGATTGTTCACCGGAAGTGCTTCTAAGCTCAAGGGCCCCCTTCGTCCCCATTCTATGTAT

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G047055_T04 (Zea mays), 3'ss of exon 4
------------------------------gtaccacaacattcttttgctcgtttttcttatcagccttgtttttctttttcgtttc---tcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                |  |   |||||   |   |     ||  |||         || |  ||| | |||     ||||||||||||||| ||| | |||||||| ||||| || || || || |||||||| || ||||||||                                   
gtaaacaaacgcagcagcggccaaaaaataaaaaaaacgcattccgatttccccaaatccgatctatacctgcttacgattttgcttccatctgcagATGTGGATTGCCAAGGCTGAGTACGACGAGTCTGGCCCGTCCATCGTGCACAGGAAATGCTTCTAATTCTTTGGGCCCAAGAGATGCAAAGCCGAGAGGA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 3
-------gtacca-caacattcttttgctcgtttttcttatcagccttgtttttctttttcgtttct---cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG
         || | |||  |||   | | | |||     ||||   |    |  |  ||| | ||      |||||||||||| || ||| |||||||||| ||||| || ||||| || || ||||| || |||||||| 
gtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G152328_T01 (Zea mays), 3'ss of exon 4
-------gtacca-caacattcttttgctcgtttttcttatcagccttgtttttctttttcgtttct---cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
         || | |||  |||   | | | |||     ||||   |    |  |  ||| | ||      |||||||||||| || ||| |||||||||| ||||| || ||||| || || ||||| || ||||||||                                   
gtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAATTCTTTGGGCCCGAGAAATGCAAGCCGTGGGGGA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 3
---------------------------------------gtaccacaacattctt---ttgctcgtttttct-tatcagccttgtttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG
                                        |   |     || |    | |  | || |||| |   |    ||     |||||   ||    ||||||||||||||||||| | || || || ||||| |||||||| ||||||||||||||||||||||| 
gtttgttctcttcctttattctttttcctgcttcttggaatgttatgttgttgtgagatagtacattcttctatgataataatgacacacttttgttttgagtgcagATGTGGATTGCAAAGGCAGAATATGACGAGTCTGGTCCATCAATTGTGCACAGAAAGTGCTTCTAA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G10170.1 (Glycine max), 3'ss of exon 4
-----------------------------------gtaccacaacattcttttgctcgtttttct----tatcagccttgtttttctttttcgtttct--cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                    |   |    ||  |      | || ||||    ||  |    ||        | | ||||     ||||||||||||||||||| | || || || || || |||||||| |||||||||||||||||||||||                                   
gtttgttctcttcattttttttcctgcttcttggaatgttatgttatcgtgagatacattcttctatgctaataataatgacacgaactgttgttttgagtgcagATGTGGATTGCAAAGGCAGAATATGACGAATCTGGTCCATCAATTGTGCACAGAAAGTGCTTCTAAACTGTTTCGATAGATAGGGTTATTGAAGGGAAAG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 3
----------------------------gtaccacaacatt--cttttgc-tcgt-ttttcttatcagccttgtttttctttttcgtttct----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                             || | | | |||  |  |||| || | |  | ||   |  ||  | ||      || | | |     ||||||||||||||||||| | |||||||||||| | ||||| || ||||| ||||| || ||||||||                                   
ttagttctagtttcgattcccagatcaattatccctatattgccagttgcatcatgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA19G00850.1 (Glycine max), 3'ss of exon 3
------------------gtaccac-aacattcttttgctcgtttttctta----tcagccttgtttttctttttcgtttct-cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                   ||  || ||    || ||     ||  | | |    |      || |      | ||| ||    ||||||||||||||| ||| | |||||||| ||||| || ||||| ||||| || ||||||||||||||                                   
gtctgtttctgttctttaatatgactaattaactattaactattgctttgaatgcttgctaatgatacaaactgtcgcttgagtgcagATGTGGATTGCGAAGGCAGAGTACGACGAGTCTGGACCATCAATTGTTCATAGAAAGTGCTTCTAAATTGTTTGGTTGATAGGGTTATTGAAGAAAAAGA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA05G09290.3 (Glycine max), 3'ss of exon 4
------------------gtaccac-aacattcttttgctcgtttttcttatcagccttgtttttctttttcgtttct-cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                   ||  |  ||    || |||||     | |||   |    || |     || ||| ||    ||||||||||||||| ||| | |||||||| ||||| || ||||| ||||| || ||||||||||||||                                   
gtatgtttctgttctttaatatgattaatgaactattgctttgaatgcttgctaa---tgatacaaattatcgcttgagtgcagATGTGGATTGCGAAGGCAGAGTACGACGAGTCTGGACCATCAATTGTTCATAGAAAGTGCTTCTAAATTGTTTGAGCAATAGGGTTATTGAAGAAAAAGA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
-------------------------gtaccacaacattcttttgct-cgtttttcttatcagccttgtttttcttt-----ttcgtttct-----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG
                           |  | ||  || ||||| |  | |    |||  ||   | ||  |  |       | |||| |      ||||||||||||||| ||| | |||||||||||||| ||||| || ||||| ||||| || ||||| |  
tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA12G06820.1 (Glycine max), 3'ss of exon 4
-------------------------------gtaccacaacattcttttgc-tcgtttttcttatcagccttgtttttctttttcgtttct----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                |     || || |   |   |    | |  |  |||     |  |      || | | |     ||||||||||||||||||| | ||||| |||||| | ||||| || ||||| ||||| || |||||||                                    
ttttcttccttttagttctagtttcggttccctgatcaaatatcccagtaagttaaatataatgccagtagcataataggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTGAATGTTGCAAGGTGGCTTGGTGAAAGAAAATACGG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA15G04360.1 (Glycine max), 3'ss of exon 3
-------------------------gtaccacaacattcttttgct-cgtttttcttatcagccttgtttttctt-----tttcgtttct-----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                            | | ||  || ||||| |  | ||   |||  ||   | ||  |  |     | |  ||| |      ||||||||||||||| ||| | ||||| |||||||| ||||| || ||||| ||||| || ||||| ||                                   
catcctcatgcaaatttgggcaaacaccctagaatgttgttttgatatggttaatttagtagggatattgatgataaggatcttatttttggaaatgcagATGTGGATTGCGAAGGCAGAGTATGATGAGTCTGGTCCTTCAATTGTACACAGGAAATGCTTTTAAATGCAGCAGAATGGCTTGGTGTAGGTACAGCGTC

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
-------------gtaccacaac---attcttttgctcgtttttcttatcagccttgttt---ttct------ttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------
              ||  ||||      |||||  | | | |  |   |        |||    |||      | ||    | | ||||||||||||| |||||   || || |||||||| |||||||| || || ||||| |||||||||||                       
gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 4
-------------gtaccacaac---attcttttgctcgtttttcttatcagccttgttt---ttct------ttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
              ||  ||||      |||||  | | | |  |   |        |||    |||      | ||    | | ||||||||||||| |||||   || || |||||||| |||||||| || || ||||| |||||||||||                                   
gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATGGTGAGTTATGTT

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA04G39380.1 (Glycine max), 3'ss of exon 4
---------------gtaccacaacat-tcttttgctcgtttttcttatcagccttgtttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                |  || |  || ||||   | ||| |  |   |         |   | | ||    | | ||||||||||||  | |||   || || |||||||| |||||||| ||||| ||||| |||||||||||                                   
gtgattgttttgtttattgcaaattatctcttccacacgtgtaccaattagattgaactaaacatgttttggttttgcagATGTGGATATCGAAGGGTGAATATGATGAGTCTGGTCCATCCATTGTCCACAGGAAGTGCTTCTAAGTCCAAAAGAAATGCTTTAATGGTGAGTTATGTT

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------gtaccacaacattcttttgctcgtttttcttatca-----------------gccttgtttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                 |   |   | |   ||  ||||  |||    | ||                    |||||||  || |  || |    |||||||||||| |||||   |||||||||||||| |||||||||||||| ||||| || ||||||||                                   
gtaaaaatcccaattccgcctctttaaaactttcagctccatttatgaaacatgagtgaaaatactgaaattttgttttgtttgtgtgtgtgaatcagATGTGGATTTCAAAGAGTGAGTACGATGAGTCAGGTCCATCGATTGTTCACAGGAAATGCTTCTAAGTGTGTCTTGTCTTATCTGGTTCGTGGTGGTGAG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv06s0004g04570.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------gtaccacaacattcttt-----tgctcgtttttcttatcagccttgtttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                   ||  ||| |||  ||     ||      |||  ||  ||   ||  | |  | || ||     |||||||||||| |||||| | ||||| ||||| || || ||||| |||||||| || || ||||||||                                   
ctatattctctgtttttcagacattttttttcctcactccaagatttgttcttgatgtagcaatttgctacaagtactgaatgtgatatttgtaat--gcagATGTGGATAGCAAAGGCAGAGTATGATGAATCTGGGCCATCTATTGTGCATAGGAAATGCTTCTAAATTGGCCAGATGGGGGAGGTAGAAGAAAGCCAGT

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------gtaccacaacattcttttgctcgttt---------ttcttatcagccttgtttttctttttcgtt-tctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                                              ||  |   | || ||   | | ||           |  || |     ||  |    ||  | ||| |   ||||||||||||||| ||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||||                                  
gtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcagATGTGGATTGCGAAGTCGGAGTACGATGAGTCAGGTCCATCAATTGTGCACAGGAAGTGTTTCTAGAGCAGTGCGACACATCTTTTGCTTTTTTCAGCAC

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------gtaccacaacattcttttgctcgtttttcttatcagc-cttgt---ttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG
                                                                        | |    |  ||  ||      |||  |    || |   |||    | || || ||  | |   |||||||||||| || || || |||||||| ||||| |||||||| |||||||| || ||||| ||||||
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG

upper sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------gtaccacaacattcttttgctcgtttttcttatcagc-cttgt---ttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
                                                                        | |    |  ||  ||      |||  |    || |   |||    | || || ||  | |   |||||||||||| || || || |||||||| ||||| |||||||| |||||||| || ||||| ||||||                                  
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAGGTAAGATGTATGTACCGCTTGACTTTTTCATGAC

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: 30 (upstream exon), 20 (downstream exon)
Score: 2

TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATTGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgtaccacaac ... tttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcttttgctcgtttttcttatcagccttgtttttctttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG
              tttttcttatcagcct  CT-rich tract
                             ttgtttttcttttt  TA-rich tract