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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

Basic information

species Selaginella moellendorffii
transcript EFJ34024
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g53540.3 (Oryza sativa), 3'ss of exon 3
------------------------------------------------gtaagtactacaagccgagagca--tgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
|| || || | | || || | || ||||| | | ||| || |||||||| ||||| || || || |||||||||||| ||||||||||||||||||| || |||||||||| ||||| |||||||||||||||||
tcctggatgcattaattcgtacgtactattaacttactgatgactaatagaattaaattaatctcggttcatctgttctaaatctatctgatctgat--cagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| || | | | || | | | ||| || | |||| ||||||||||||| || ||||| ||||| |||||||| | | ||||||||| ||| || || || | ||||| || |||||||||||||||||||||
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatg---cagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------------------------------gtaagtacta--caagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
|| | | | | | || | | || | | | || ||| || ||||||||||| || || || ||||| ||||||||| ||||||||||| ||||||| || || || |||| ||| || || |||||||| |||||
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os06g10600.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatctttctt---cgtgc----cagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | | | ||| | | | | | | ||| || |||| |||| ||||||||||||| || || || ||||| || ||||| | |||| ||||||||||| || ||||||| |||| ||||||||||||||||||||
gtacgcgttttctctatttttttttctgctgttgttcttctatgtgttgttggctttcgtccgccatggcggcggcgccatggatggagggatgaaatggtgcgtgtgtttgtttcccgtgttgtgcagGATGTTCAAGGAGTGCCCCCACCCGGACGAGAACCAGCGGGCGCAGCTTAGCCGGGAGCTCGGGTTGGAGCCGAGGCAGATCAAGTTCTGGTTCCAGAAT

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G122897_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------gtaagtactacaagccgagagcatgat-gagaacttatctttcttcgt--gccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | | || ||||| | | || | | ||||| || ||||||||||| || || || ||||| ||||||||| ||||||||||||||||||| || |||||||| | || ||||||||||||||||||||
attccatattttgtagaaacattaattaatccgccgtcactcacggaacacgtcatcttttgatctgatgatcgtcggttcatgcatggatgatggccagTTTCTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGCAAGGAGCTGAGCCGGGAGCTGGGGCTGGAGCCCCTCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 3
----------------------------------------------------------gtaagtactacaagccgagagcatga-tgagaacttatctttctt----cgtg-----ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
||| | ||| | || |||| ||| || | | || ||| ||| || |||||||||||||| || || || || |||||||| ||||||||||||||||||| || || ||||| | ||| ||||||||||||||||||||
gtaaggacaatgacatgaacactcttcttcttcttccctagctagctttaagcaccatttaaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G004957_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------------gtaagtac--tacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| || | || | | | || || | || | |||||| |||||||||| || || || ||||| |||||| | ||||||||||||||||||| || |||||||||| || ||||||||||||||||||||
gttgagtcgtccctccaatctagctagctagtatctactatctagagtgatcggtgcggtatttgacatggttgtgcgccaaatggacggatccaccgtgcagGTTCTTCAAGGAGTACCCGCACCCTGACGACAAGCAGAGGAAGGAGCTGAGCCGGGAGCTGGGCCTGGAGCCTCTCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G130442_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtg-----ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | | | | || | | || | | | | ||| |||||| ||||||||||| || || || ||||| |||||||| ||||||||||||||||||| || || ||||| | ||| |||||||| |||||||||||
gtaagaacgatagcttgagctccccttcctctaagcatgcaccatttgaaaggattcattttcgagatagatagataatttcatttcattcattaaaaatcgtgtctgattgtttaattggggacgactgtgaattgtgattggtcagGTTCTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGAAGGAGCTGAGCCGGGAGCTCGGCCTCGAGCCGCTGCAGGTCAAGTTTTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G062318_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------gtaagtact-----acaagccgagagcatgatgagaacttatctttcttcgtg---ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
|| ||| | | | || || | | | | || ||| |||| ||||||||||||| || || |||||||| || |||||| | ||| ||||||||||| || |||||||| || || |||||||||||||||||||
gtacggttctctctcgtttcgttttgtttccatttcttttgctgtttcttcgttctgtccggtccggccaccgccctcgtggttgttgacggccggcgtcgtcgtgagtcttgatgaattgacggaaaggaatgtaatggtgcgtgttcgccggtgaccgcagGATGTTCAAGGAGTGCCCGCACCCCGACGAGAACCAGCGCGCCGCGCTCAGCCGGGAGCTCGGCCTGGAGCCGCGCCAGATCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G126646_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------gtaagtactacaagc--cgagagcatgatgagaacttatctttcttcgtgcc---agGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
|| | || || || | | | || | || ||| ||| ||||||||||||| || || || ||||| || ||||| | |||||||| ||||||| || |||||||| ||||| |||||||||||||||||||
gtacgtgccgatttacccccctctccctctctccattatctactgcgtgcctggttagtggttagccgtacgtgtttgttcgttttggatgctttgctcaaatggcggcggcggcggcggcgtttgccttgtctgtgcttgtgcgcgcccgcagGATGTTCAAGGAGTGCCCGCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G145690_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------gtaagtactacaagccgagagca-tgatgagaa-cttatctttcttcgtgc-------cagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | || | | || | | ||| ||| | |||| |||| ||||||||||||| || || || ||||| || ||||| | |||||||| ||||||| || |||||||| ||||| |||||||||||||||||||
gtacgtgcaccctgctggccggcaggcctgcgccgatttccccctcccttccgtccttatctactggctggtttggttagctagctgtacgtgtttgctcgttttggctgctctgctcaaatggcggcggcgtctgtcttgtctgtgcctgtgcgcgcccgcagGATGTTCAAGGAGTGCCCGCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G001289_T02 (Zea mays), 3'ss of exon 2
-----------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtg-ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| || | | | | | ||| || | | || |||| || |||||||| || || || || ||||| ||||||||| |||||||||| |||||||| || |||| || | || ||||||||||||||||||||
tattattccatattttctagaaacattaattcattcgtcaatcactcacactcacaaaatactcatcttttcttgaaaattgggttcaacggatggccagTTTCTTCAAGGAATGCCCGCACCCGGACGACAAGCAGCGCAAGGAGCTGAGTCGGGAGCTGGGTCTGGTACCCCTCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------gtaagtac-tacaagccgagagca-tgatgagaacttatctttcttcgtgc---cagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | | || | | | ||| || | | | | | | | | |||| ||||||||||||| || || || ||||| |||||||| | | ||||||||| |||||| || || | || || || ||||||||||||||||||||
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AC235534.1_FGT007 (Zea mays), 3'ss of exon 2
-----------------------------gtaagtactacaagccgagagcatg---atgagaacttatctttcttcgtgcc--agGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
|| | || || | | | | | | || || || | ||||| ||| |||||||||| | | || || ||||| ||||||||| | |||||||| || |||| || ||||| || ||||| ||||||||||||||||||||
gtgagcgcccccgcgtggttcgattcgtcgtgttttcttgaacttgcgtgaaggcccgcgctcacgcgtcgatcgttgtgccgcagGATGTTCAAGGAATTCCACCACCCGGACGAGAAGCAGCGCGCGCAGCTGAGCAGGCAGCTGGGCCTGGACCCGCGGCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA16G32130.1 (Glycine max), 3'ss of exon 1
----------------------------------------gtaagtactacaagccgagagcatgatgaga---acttatcttt-----cttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
|| | || | | || | || | || | ||| || || ||||| |||||||||||||||||||||||||| ||||| | || || ||| | ||| || ||||| |||||||||||||||||| ||||||
gtatggctctataaaattctgaaatctttttttacaaactgtgattatctgtattgatttgtttgttaaggttgatttttttttgctgtttttgttttagGTTTTTCAAGGAGTGTCCTCATCCCGACGAGAAGCAAAGAACAGATCTTAGCAAGAGGCTTGGCTTGGAGAACAAGCAAGTCAAGTTCTGGTTTCAGAAT

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA03G01860.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | | | | | | || | | || | ||| | | |||||||||||||||||||||||||| || || ||||| | | || ||||| | ||| | |||| |||| || || ||||| |||||||| |||
aatctgttttttctctcgacgtgtaaccaaacacactctatcatgttatttgaatggtggatgatgttttt-tgttttgtttttttatttatgaattttagGTTGTTCAAGGAGTGTCCTCATCCAGATGAAAAGCAAAGGCTTGAACTGAGTAGAAGGCTGTGTTTGGAAACTCGTCAGGTGAAGTTTTGGTTCCAAAAT

upper sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA07G08340.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatc--tttcttcgtg----ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
| | || | || | ||||| || | ||| || || |||||||||||||||||||||||||| || || ||||| | | || ||||| | ||| | |||| |||| |||
tacttcttaatcagtttttcactagacgtgtaaccaaacacactctattatatgatttgaatggtggatgatgtttttttaattttttgatgaattttagGTTGTTCAAGGAGTGTCCTCATCCAGATGAAAAGCAAAGGCTTGAACTGAGTAGAAGGCTGTGTTTGGAAACTCGTCAA---------------------

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), 35 (downstream exon)
Score: 53

GCAGCGAGAACATGGGAAACGCGTCGGGTGACGAGCAGGAGCCGCCGAGGAAGAAGCGCTATCATCGTCACACTGCAAGGCAGATTCAAGAGATGGAATCgtaagtacta ... ttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
                                     cttatctttcttcgt  CT-rich tract
 ttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT