Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaattcctttgctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT

Basic information

species Selaginella moellendorffii
transcript EFJ36434
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 2
--------------------gtgaaattcctttg--ctttattcatgttc---ttcgcgggga------tttagttcgttagtgtgtgacaatttc-cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                     | ||||   |     | ||   || | ||   |   | | ||      ||| |||    |          ||||  |||||||| || ||||| ||||||||||||||||| || || |||||||||||  | || || || || |||||||| || ||||||||| ||||||| ||||
ccttttctccacttctcacaataaaatatttgcagacattgcacacgatcaactctccagtgaaataatttttgtttaccatctcaacttgattttgcagATTAGGAGCCATGCACAGAAGTATTTTTTGAAGGTTCAAAAGAATGGAACAAGTGAGCATGTCCCACCTCCACGACCAAAGCGTAAAGCTGCTCATCCAT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 2
-------------------------gtgaaattcctttgctttattcatgttcttcg-cggggatttagttcgt----tagtgtgtgacaatttc--cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                          ||   || |||     ||     ||  | |  | |  ||   || | |    ||   |      || |   ||||| ||||| ||||| |||||||| |||||||| || || ||||||||||| || || ||  | || |||||  |||| || || ||  | || || ||||
tactccaataagtaaatgaacatgtttgtttttgcttaatagtaaatcggtaatgcatctgacataccgtgcatgatctaaaatacagttatcttaacagATCAGAAGCCATGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCAT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 2
-------------------------gtgaaat--tcctttgctttatt--catgttcttcgcggggatttagttcgt-tagtgtgtgacaatttc--cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                         || || |  | | |   ||| ||   ||||| |     |   | |   |  | ||        |  |||   |||||||| ||||| || |||||||| |||||||| || || ||||||||||| || || ||  | || || ||  |||| ||||| ||  |||| || ||||
cactgtcgtcttgctattccaagacgtaaattggttcctgattttcttgttatgttgtctaacgaactgtgcatgatctaaacaacagctcttttaacagATTAGGAGTCACGCACAGAAGTACTTTTTGAAGGTTCAAAAGAATGGAACAGGTGAGCATTTGCCCCCACCTAGGCCAAAGCGAAAGGCTGCCCATCCAT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA19G36170.1 (Glycine max), 3'ss of exon 3
---------------------------gtgaaattcctttgctttattcatgttctt-cgcggggatttagttcgttagtgtgtga-caatttccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                            |  |||| || |  | | || |||   ||  |  |    |      ||       |||    | | |||||||||||||||||||||||||| || |||||||| || ||||  || || | || ||| || |||||||| ||||| ||||| ||| || |||| || |
gttaggaaaaagctcttcagctatgtgttctaatttctatcttctgtt-atgccattatgttgtatctctcacagtctcaccatgagttttcttcagATTAGAAGTCATGCCCAGAAGTACTTCTTGAAAGTTCAAAAGAGCGGGACAGTAGCACATGTGCCTCCTCCTCGGCCTAAGCGCAAAGCTTCTCATCCTT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA03G33440.1 (Glycine max), 3'ss of exon 2
---------------------------gtgaaattcctttgctttattcatgttcttcgcggggatttagttcg---ttagtgtgtgacaatttccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                            |  |||| || |  | | || |||   ||     | || |    |    | | | |       | | ||||| |||||||||||||||||||| || |||||||| || ||||| ||  | | || |||||| |||||||| ||||| ||||| ||| || |||| || |
gttaggaaacagctcttcagctaggtgttctaatttctatcttctgtt-atgccattatgttgtatctctcacagtctcactattaagttgtcttcagATCAGAAGTCATGCCCAGAAGTACTTCTTGAAAGTTCAAAAGAACGGGGCAGTAGCACACGTGCCTCCTCCTCGGCCTAAGCGCAAAGCTTCTCATCCTT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA07G07200.1 (Glycine max), 3'ss of exon 2
------------------------gtgaaattcctttgctttattcatgttcttcgcggggatt-tagttcgttagtgtgtgacaatttc-------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                        |||       | ||     | ||||||| ||     |    |  |||  |  | ||||  || |||       |||||  |||||||||| |||||||||||| | ||||| |||||||| |||||  | ||||| || |||||||| ||||| ||| | ||| ||||||  ||||
agtgtttctttcatcaattttcttgtgcttaatatctgacacttacatgttcctctaactgtccattcttcactgttctgtgtaaaattctatttggcagATACGAAGTCATGCACAGAAGTATTTTCTTAAAGTTCAGAAGAAGGGAACAAGTGAACATGTACCTCCTCCCCGGCCAAAGAGAAAAGCTGCTCGCCCAT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 2
---------------------------gtgaaattcctttgctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttc-------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                           || || ||| |   |||   |  | ||||      | |||   |||  |  | | ||  || |||       |||||  |||||||||| || ||||||||| | ||||| ||||||||||||||  | ||||| || |||||||| ||||| ||| | ||| ||||||  ||||
agtgtttatttcaccaattttcttgtggtaaatttcttacacttacatgttcttctaactatgcattc--ttcactgttctatgtaaaattctatttggcagATACGAAGTCATGCACAAAAGTATTTTCTTAAAGTTCAGAAGAATGGAACAAGTGAACATGTACCTCCTCCTCGGCCAAAGAGAAAAGCTGCTCGCCCAT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA18G47230.1 (Glycine max), 3'ss of exon 2
---------------gtgaaattcctttgcttta------ttcatg-ttcttcgcggggatttagt-tcgttagtgtgtgacaatttc---------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
               ||    || |||| | |||      ||  || ||||   |     || ||  | | | || ||   |  || |         ||||| || |||||||| |||||||||||  ||||||| ||||||||||| ||  | ||||| || ||||| || || || ||| | ||| ||||||| || |
atagtaaaatacagtgtagcttttcttttccttaatgtatttggtgcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G05560.1 (Glycine max), 3'ss of exon 2
-----gtgaa-attcctttgctttattcatgttcttcgcggggatt-tagttcgttagtgtgtgacaattt---ccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
     ||||    |  ||   | | |  || ||||   |||| ||| |   ||  ||  |  | ||  |||     ||||| |||| ||||||||||| || || |||||||| || |||||||| ||||  | ||| || |||||||| || || ||||| ||| ||||||| || |
gtacggtgactgctttttcagtatgtctatattctatacgggcattatttgtcactaacgaattactttttgttatagATTCGAAGCCATGCCCAGAAATACTTCTTGAAAGTTCAAAAGAATGGGACTGTGGCACATGTGCCTCCTCCCCGTCCAAAGCGCAAAGCTGCTCATCCTT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv08s0040g03220.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------gtgaaattcctttgctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttc----cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                            || || ||    |   || |||||| |  |  |    ||||||||  ||  |       | || |    |||||||| |||||||||||||| || ||||| || ||||| |||||||| || | || ||| || || || || || || ||||| ||| ||  ||| || |
tgctctgtgtgctgtaatttgttattaagtaaagtttggctctattgttcatggtggtttcatttatttagtttttttatactgagtatttgcattgcagATTAGGAGTCATGCCCAGAAATACTTTTTAAAGGTCCAAAAGAATGGGACAGTAGCACATGTGCCACCGCCTCGCCCAAAGCGCAAAGCTATTCATCCTT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S46_272V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------gtgaaattcctttgc-----tttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttc---cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                           || ||    |       |  |||||| |||||   |  | | |  ||  |   |      || |||    |||||  ||||||| || || || |||||||| ||||| ||||||||||||||||| ||||| |||||||| ||||| ||||| || || || ||||||||||
ccaaggtcagtttatgcgaccaaaacaaacttggcctatagaagtgaattcattttcttattgtcggtgttatttatctttaaaatccatttttatgcagATCCGAAGTCACGCTCAAAAATATTTTTTAAAAGTACAGAAGAATGGAACTGGGGAACATGTTCCTCCGCCACGACCGAAACGCAAGTCAGCTCAACCAT

upper sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------------------------gtgaaattcctttgc-tttattcatgttctt---cgcggggatttagttcgttagtgtg--tgacaatttccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                                                                                                                      |||    | | ||  | ||  |||     |     || ||| |||    |  | |||   |||   ||| |||||  |||||||||| || || |||||||| ||||| || || |||||||||||||| || || ||||| ||||| || || || || || | |||||| |
gtactgtgtcgttggttttattgctgtttcagctaggaaatatcagcacttcaatccgttgcatatcggcttgtaacctagccgcaacagagtttcagcagccatgcagtttctacattgatgggcttgtgtatgtacacataaatataaatacgtggacttaacatgcaaatgtaattgattctttgcagATCCGAAGTCATGCACAAAAATATTTTTTAAAAGTTCAAAAAAATGGAACTGGAGAGCATGTCCCTCCACCACGCCCTAAACGCAAGTCAGTTCAACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
                                                tttcc  CT-rich tract
                        atttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaattcctttgctttattcatgttcttcgcggggatttagttcgttagtgtgtgacaatttccagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC