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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ17708
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
--------------------------AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgctt-gcag--------------
                          || | ||||| | |||||| || |||||||| ||||||||||| ||| | ||||| || || || || || ||  ||||||| ||||||||||||||||||||   |      || |  |       |   ||   |||     |  |     ||  | |              
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
-----------------------------------------AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttgcag-
                                         || | ||||| | |||||| || |||||||| ||||||||||| ||| | ||||| || || || || || ||  ||||||| ||||||||||||||||||||   |      || |  | |  |     || |   |||    ||       ||  |  
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgct-tcgctcgcccaatctctttcgaaccagtaaaattttacc

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os01g01060.1 (Oryza sativa), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctc----tttgttacaacttca----ttgatttttcg-tccttcctgcttgcag--------------------------------
|| | |||||||  ||||| || |||||||| ||||||||||| ||| | ||||| || || || || |||||  ||||||| || |||||||||||||||||   |  |  |  ||    ||  || ||  | |     |  ||| | |  | |    |  || ||                                 
AGATCATGGCTGTCCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATCCAGGTCATCGTAGATGCCATCATCAACAGgtaccaccgtccaattcccaattcctttcagttgcgcacttcaattgtccaattcacttttttttcaatcaccctcaccctcttatatgcaaatgcttat

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgctt-gcag----------------------------------------
|| | ||||| | |||||| || |||||||| ||||||||||| ||| | ||||| || || || || || ||  ||||||| ||||||||||||||||||||   |      || |  |       |   ||   |||     |  |     ||  | |                                        
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G078985_T01 (Zea mays), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttgcag------------------------------------------
|| | ||||| |  |||||  |||||||| |  |||||||||| ||| ||||||| || || ||||| |||||  |  ||||||||||||| |||||||||||   |  | | |||| |     ||    |  |   | |     |   ||  |  |||                                          
AGGTCATGGCCGTCCGCATCATGAAGCACACCCTGGAGATCATCCACCTGCTCACTGACGCCAATCCCATCCAGGTGGTCGTGGACGCCATTATCAACAGgtactacctt-gctctcctgtcctcactcccgatctctgtattgtcaggctaataacagctaaacttgttactttatgctgatactttttggaatgcggta

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G156673_T02 (Zea mays), 5'ss of exon 1
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctc--tttgttacaacttcattgatttttcgtcct-tcctgcttgcag---------------------------------------
|| | |||||||  |||||  | |||||  |  |||||||||| ||| ||||||| ||||| || || |||||  || |||| ||||| |||||||||||||| ||   || |||||   |  | ||   |  |   | |  |     | |  || || ||                                        
AGGTCATGGCTGTCCGCATCATCAAGCATACCCTGGAGATCATCCACCTGCTCACCGATGCCAACCCCATCCAGGTCGTCGTCGACGCGATCATCAACAGgtacagtctta-atctcggctaataaccgttaaacctactcgttactatatgttgattccattcagtatgctggatccccccctgaaccgtgtgtgtattt

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctat-----agatctcttt-gttacaacttcattgatttttcgtccttcctgcttgcag-----------------------------------------------------------------------------------------
|||||||||| | |||||| ||||||||||||||||||||||| ||| |||| || ||   ||| || |||||  |||||||||| |||||||||||||||||| | |||     | |  | ||| | | ||  ||    |      ||        ||     |                                                                                         
AGTTGATGGCGGTGCGCATCGTGAAGCACGCGATGGAGATCATCCACCTGCTGACGGACCAGAACCCCATCCAGGTCATCGTGGATGCCATCATCAACAGgtag-gttatctcgaacacttgtttagctgcatattggggggagaggcgggggatgggcgcatgggcgggaggagaggttgcaacaggaatttagggttatgcgggatgatgtggggctcgggagctgagaggtcgcggtgggaatgggtacag

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S400_33V6.1 (Physcomitrella patens), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcatt---gatttttcgtccttcctgcttgcag-------------------------------------------------------------
||||||||||||  ||||||||||||||||| ||||||||||||||| | || || |||  ||| || |||||  ||||||| || || |||||||||||||     | |  |||| | | ||     || ||     |  |    | |  |   ||||  |                                                             
AGTTGATGGCTGTCCGCATTGTGAAGCACGCTATGGAGATCATTCACCTTCTGACTGATCAGAACCCCATCCAGGTCATCGTTGATGCTATCATCAACAGgtttgaatctt-atctttctattggtgtttgatgtggaaaatgaaatgcgacactcttgaggcgagtctaattcaattgtagcaatttttagtggcatgaggcatatcttttatctgctgcag

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S101_208V6.1 (Physcomitrella patens), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctat--agatctctttgttacaacttcattgatttttcgtccttcctgcttgcag---------------------------------------------------------------------------------------
||||||||||||  ||||| |||||||||||||||||||| |||||| | || || ||   ||| || |||||  ||||||| ||||||||||||||||||| |          |  ||  ||      |      ||  |||      |   || ||                                                                                          
AGTTGATGGCTGTACGCATCGTGAAGCACGCGATGGAGATTATTCACCTACTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcag

upper sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 5'ss of exon 2
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttac--aacttcatt--gatttttcgtccttcctgcttgcag----------------------------------------------
||||||||||||  ||||||||||||||||| |||||||| || ||  | || || ||   ||| || || ||  ||||||| || || || ||||||||||   |    |   |  | || ||   ||| || |   ||          || ||| ||  |                                               
AGTTGATGGCTGTCCGCATTGTGAAGCACGCCATGGAGATTATCCATCTCCTGACTGACCAGAACCCCATTCAGGTCATCGTCGATGCTATTATCAACAGgttcggacgcaatcccgtgtgatatcgaacatcctgaggacacaattctttttctgattaaatattgtcaatttgtctctgagcgacagtgttttcccatacattgcag

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|169098900|gb|FE502297.1|FE502297
EST:     CTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAG                         TGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCG
genomic: CTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctat ... ctgcttgcagTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCG




















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), 35 (downstream exon)
Score: 94

AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctat ... ctgcttgcagTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGTCGCGTGAATCAAGCCATTTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG