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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcactgccttacgaaacagcctgcattcttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT

Basic information

species Selaginella moellendorffii
transcript EFJ27687
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 4
---gtgcactgccttacg----aaacagcctgca-ttcttatttacaaggcgaattt--ttcttttt-------------cagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
    | ||| |    |      ||| |  ||| | || || ||| | | |  || |   ||| || |             |||||||||| |||||  |  | ||||||||||| |||||  |||||||||| ||||| |||||||| |||||| | ||||| ||||| |||||||||  |||
gtaattcacagttgaaaaataaaaataatctggaattgttgttttccaagataactcagttcattctattgatcttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGGAACCATATCCTCTAGACATGAGAGGAGAATTGGACGACACAGCTGCCTT

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------gtgcactgccttacgaaacagcctgcattcttattta--caaggcga-atttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
                                                    ||  | ||   ||  || |    ||   | | || ||  ||     | ||  | | ||| |||||||||| |||||  |  |||||||||| || || ||  | |||||||| || |||||||||||||||||| | ||||| || |||||||||||    ||
gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------gtgcactgccttacgaaacagcctgcattcttattta--caaggcga-atttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
                                                           ||  ||||    ||   | | || ||  ||   | | ||  | |  || ||||||| || |||||  |  |||||||||| || || ||  | |||||||| || |||||||||||||||||| | ||||| || |||||||||||    ||
gtattaaagatgcatatagaattcacttttcatttgttgtaatgttttagttgtaaatgtaataaacgtattggtctatcatgtatccataacaatatgctcccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 4
--------------------------------gtgcactgccttacgaaacagcctgcattctta-tttacaaggcgaattt-ttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
                                 || | |   |       |||  |  |  || |   ||  | ||  |||  ||||||| |||||||||| |||||  |  | |||||||| || ||||| ||||| ||||| ||||||||||||||||| ||| | |||||  | ||||||||||||   ||
gtactcactcttgcttttcaaaggcagacagtttgtagttgttgcttttccagtttcaacactcaacataagatgctcattggttcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTGAACCGTATCCTCTGGATATGAGAGGAGAACTAGATGACACAGCTGCTTT

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------gtgcactgcc----ttacgaaacagcctgcatt--cttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
                                               | | |||     |  | | |   ||||  ||  | | || | |||    ||  | | | | |||||||||| |||||  |  | ||||||||||| |||||  |||| ||||| || || ||||||||||||||| | |||||  | |||||||||||    ||
gtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgataagaaatatgctccatctccagACTTGGATTTCTCATTTCTTGAGATGAATCCGTTCACCATGGTCAATGGGGAGCCATATCCTCTGGACATGAGAGGAGAACTAGATGACACAGCAGCTTT

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------gt-gcactgccttacgaaacagcctgcattcttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
                                                              || ||| |    |   ||        |||| |  ||| | |      ||  || | || |||| |||| ||  || |  | ||||||||||| ||||||||||| |||||  | || ||||||||||||||| | || ||  | |||||||| |||   ||
gtatgctacaaaatatgcatttattaacattagatgtgcttgtgaagacaacttcattgatggtagcatttaagtttaaagttttaaacattttcttttcctattttttttcctcgtgtt-agACCTGGATTTTACTTTCTTGGAGATGAATCCTTTCACTTTGGTCAATGGAAAGCCTTATCCTCTGGACATGAGAGGCGAACTTGATGACACTGCTGCTTT

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G17010.2 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------gt-gcactgccttacgaaacagcctgcattcttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
                                                              || ||| |    |   ||        |||  || ||| | |      ||  || | || |||  |||| ||  || |  | ||||||||||| ||||||||||| |||||  | || ||||||||||||||| | || ||| | ||||| || |||   ||
gtatattacaaaatatgcatttactagcattagatgtgctttagaagacaacttcattgattgtagcatttaaatttaaagttttaaacatatttttttcctattttttttcctcatgtt-agATCTGGATTTTACTTTCTTGGAGATGAATCCTTTCACTTTGGTCAATGGAAAGCCTTATCCTCTGGACATGAGAGGCGAGCTTGATGATACTGCTGCTTT

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|169064651|gb|FE471382.1|FE471382
EST:     TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169067518|gb|FE475260.1|FE475260
EST:     TCGTGGCAAGATTGAGACGTTCATAAGAGGAGTTTTTAGCGTCTTTCAAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169071278|gb|FE478410.1|FE478410
EST:     TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAG                         GCTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169044047|gb|FE451633.1|FE451633
EST:     TCGTGGCAAGATTGAGACGTTCATAAGAGGAGTTTTTAGCGTCTTTNCAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169037362|gb|FE443308.1|FE443308
EST:     GTTCATAAGAGGAGTTTTTAGCGTCTTTCAAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: GTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169112908|gb|FE514660.1|FE514660
EST:     TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAG                         GCTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169039922|gb|FE447608.1|FE447608
EST:     TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169102324|gb|FE506548.1|FE506548
EST:     TCGTGGCAAGATTGAGACGTTCATAAGAGGAGTTTTTAGCGTCTTTCAAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
EST: gi|169112110|gb|FE513453.1|FE513453
EST:     TCGTGGCAAGATTGAGACGTTCATAAGAGGAGTTTTTAGCGTCTTTCAAG                         ACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG
genomic: TCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCG

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), 32 (downstream exon)
Score: 6

ATTCGTGGCAAGATTGAGACGTTCATAAGGGGAGTTTTTAGCGTCTTTGAAGgtgcactgcc ... tctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccttacgaaacagcctgcattcttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT
  gccttac  putative branch site (score: 6)
                                         tttttctttttc  putative PPT
                                       aatttttctttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcactgccttacgaaacagcctgcattcttatttacaaggcgaatttttctttttcagACTTGGACTTCTCTCTGATCGAGATGAATCCCTTCACTTTGGTGAATGGCGAACCGTATCCTCTGGACATGCGTGGAGAGTTGGATGACACAGCTCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC