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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttttaatccttttcgttccctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC

Basic information

species Selaginella moellendorffii
transcript EFJ20301
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 3'ss of exon 4
------------------------gtgctttttaatccttttcgttccctcctagtgtatgcattaact-gcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                        ||   || | | | |   | | |  |  ||  | ||| | |   | |  | |   |   |||| ||| | ||  | || || || ||||||||||||||||||||| | || || ||||||||||| || || ||||| |  || |||||||| ||| |  
gtgagtcagtacctgtgctacttagtaacttcttagcttgggcttccagtaataaggcatgtaatgttttgatgataaatcatagGATGGTAACCCCAGACTGTCGTGCTTCGGTCTGATGAAGAACAGCAGGGATGGGAAGAGCTATAGTACCAATTTGGCTTTCACGCCTCCTGAGTACCTTA

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G026767_T01 (Zea mays), 3'ss of exon 3
------------------------------------gtgctttttaatccttttcgttccctcctagtgtatgcattaactgcagctgtt----ttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                                    ||  ||||  |   | ||  || |   | |   | |  | | |         ||    |||||| | ||||| || || || || || || ||||||||||| |||||| | || || || ||||||||||||||| | |||||||||||||| |||||  || 
taagttgatactcctaattgcatccagttgttgaatgtcattttgtactgtcttattttcaaacaaaaatgtctagttataatgaactttctggttgcagAATGGTGACCCTCGGCTGTCATGCTTTGGTCTGATGAAAAACAGCAGGGATGGAAAAAGCTATAGCACGAACCTAGCATATACACCTCCAGAATATCTGA

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G177445_T01 (Zea mays), 3'ss of exon 4
--------------------gtgcttttta-atccttttcgttccctc-ctagtgtat----gcattaactgcag--ctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                     |||||   | ||| |||         | ||||| | |    |  ||||| |  |  |  ||||| |||| ||| | ||  |  | || ||||| ||||||||||||||||||||||| || |||||||| || || || ||||| |  || |||||||||||  |  
gtaggtcttgtttaccttagttgcttcccagatcttttatacaaaagcgctagtctttttttgttttaaccgtggaccaattttgtagGATGGTAACCCAAGATTATCATGTTTTGGTCTGATGAAGAACAGCCGAGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAATATCTTA

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G121826_T01 (Zea mays), 3'ss of exon 4
---------------------------------gtgctttttaatccttttcgttc-cctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                                  ||  |||| || |    | ||  |||  | |||| |  |||   ||   |  ||||  |||| ||| | ||  | || || ||||| |||||||||||||||||||| || || |||||||| || || || ||||| |  || |||||||| ||  |  
gtgggtctttacttgttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattg--tgggccaattttatagGAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTA

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G127050_T02 (Zea mays), 3'ss of exon 3
---------------------------------------gtgctttttaatccttttcgttccctcctagtgtatgcattaactgcagctg-ttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                                        || || | || |  |     ||| || |    |   ||   | |  |  |  || ||||| | |||||||| || || || || || || |||||||| |||||| | || || || ||||||||||| ||| | |||||||||||||| ||||| ||| 
tctttgtgatgacaacgattgcatgttacattactttgcatgtttctcaaactgtaataatccttcatgtgatgaacaaccaatataatttcttctgcagAATGGTGATCCTCGTCTTTCATGCTTTGGCCTGATGAAAAACAGCAGGGATGGGAAAAGCTATAGCACAAACCTTGCATATACACCTCCAGAATATTTGA

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
---------------------------------gtgctttttaatccttttcgttc-cctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC----
                                  ||  |||| || |    | ||  |||  | |||| |  |||   ||   |  ||||  |||| ||| | ||  | || || ||||| |||||||||||||||||||| || || |||||||| || || || ||||| |  || |||||||| ||  |      
gtgggtctttacttgttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattg--tgggccaattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------------------------------------gtgctttttaatccttttcgttccctcc-tagtgtatgcattaa----ctgcagctgttttg-cagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                                                                                                                                     | |||| ||         |    ||  |||  |||  ||| |    || |  |   |||| ||||| || |||||||||||||||||||| || || ||||||||||| || || || || |||||||| || ||  |||| || || || |||||||||||  
gtattgctcttctctgtagcagttttgaactaaaacttggtatgtcccttcccgttcctatcaagtctcgacaatcctgctatacagaacacccacatcaaatacgctaatcacttttttttacggaaaataaggttttaaagtagacctatctaatctgtagattataaattgatggtctcccacgcctttgtcagGAAGGAGATCCGCGCCTCTCTTGTTTTGGCCTCATGAAGAACAGTCGCGATGGAAAAAGCTATAGTACCAATCTGGCCTACACTCCCCCTGAATACTTAA

upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------gtgctttttaatccttttcgttcc--ctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                                      |||  ||| ||      |   |      |  ||| |||  |  |    |  |  ||||| ||||||| || || || ||||| ||||| || || |||||||||||| |||| || || ||||| ||||| || ||||| || || |||||||| |||||| 
tcgtgtgggtttcctttggaaatagttctacttagtacgtggatttcaactgcagttaatagaatgctcagtatattaacgattctctacgattttgtagGACGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGA

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|169075974|gb|FE480982.1|FE480982
EST:     ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAG                         GACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
genomic: ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAGgtgcttttta ... tgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
EST: gi|169097974|gb|FE498771.1|FE498771
EST:     ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAG                         GACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
genomic: ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAGgtgcttttta ... tgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
EST: gi|169102668|gb|FE504461.1|FE504461
EST:     ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAG                         GACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
genomic: ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAGgtgcttttta ... tgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
EST: gi|169082053|gb|FE490565.1|FE490565
EST:     ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAG                         GACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC
genomic: ACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAGgtgcttttta ... tgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGAC

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), 34 (downstream exon)
Score: 39

GAGAGTGGCTCTCTACATTGCACAGGCACTGGAGCATTGCAGCAATAATAACCGTCGTTTATATCACGACTTGAATGCGTACAGGGTCTTGTTTGATCAGgtgcttttta ... tgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatccttttcgttccctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC
                                cattaac  putative branch site (score: 39)
                                            ctgtttt  putative PPT
                                 attaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttttaatccttttcgttccctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT