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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgcttcaacacacaactaacacagctagtcaaatacag

Basic information

species Selaginella moellendorffii
transcript EFJ07179
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgagttgaat-gcttcaacacacaactaacacagctagtcaaatacag-------------------------------------------------------------------------------------------------------------------
 || || |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || |||||||| ||||| || || ||||| |        | |  |||     | |    || |     |  |||| | |||                                                                                                                   
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgt--------aatatgagttgaatgcttcaacacacaactaacacag-------ctagtcaaatacag--------------------------------
 || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || || |||||        ||    ||||  ||| || |  | | | |  |    |       ||   || ||  ||                                
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactgaaacatatccaaacttaa

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G379271_T01 (Zea mays), 5'ss of exon 3
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgt--------aatatgagttgaatgcttc----aacacaca-actaacacag-ctagtcaaatacag---------------------------------
 || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || || |||||        ||    ||||  ||| ||     ||  ||||   | |   |  ||   || ||  ||                                 
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgtttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcgtacactgaaaaatatccaaacttaat

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G036290_T01 (Zea mays), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaa--tatga------gttgaatgcttca-----acacaca-actaacacag-ctagtcaaatacag--------------------------------
 || || ||||| || || ||||| ||||| ||||| |||||||||||||| ||||| || || || ||||| || |||||||| ||| | || || ||||| |    |||      |||| ||  || |     || ||||   | |   |  |||  || ||  ||                                
AGAAGTTATTGAGGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAATCTATCATACACTCTATGGTTGAAACCCAGgtgagccctgaaccatggttgtatcttttactaaaacgcacatgttgaggtattctacccagatgtagtgctttgtacactaacatatccatgcttaatc

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaata--tgagttgaatgct----tcaacacacaacta-acacagctagtcaaatacag----------------------------------------
 || || |||||||| || || ||||||||||||||||||||| | ||||| ||||| || ||||| ||||| || ||||| || ||||| || |||||||||  |      ||  ||| |    | |   ||     | |  ||  || ||  |||||                                         
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtataaaccttattctatgttatgtttactgcattttgatatccatatattcggatacaaatggatgaggaaccatagccatagcacctacaagttccag

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgt---aatatgagttga----atgct--tcaacacacaacta-acacagctagtcaaatacag-------------------------------------
 || || |||||||| || || ||||||||||||||||| ||| | ||||| ||||| || ||||| ||||| || ||||| || ||||| || ||||||||   ||| | | |  |    ||| |  | | | ||     | |  ||  || |   || ||                                      
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtctaaatctaattctatgttatgttggttaccgcattttaatatccatatatttggatgcaaatggatgaggaaccatagtacctacaagctacaagtt

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgct--tcaacacacaactaacacagctagtcaaatacag-------------------------------
 |||||||||||||| || ||||||||||||||||| ||||| || || || ||||| || ||||| |||   || ||||| |||||||| || ||||||||  |        | | ||    ||   |  | |    | | |    ||| | |                                
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: EDP02894 (Chlamydomonas reinhardtii), 5'ss of exon 8
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGg--taatatgagttga-atgcttcaacacacaactaacacagctagtcaaatacag-----------------------------------------------------------------
                       |||| ||||  ||||| ||  |||| ||||| || ||||| ||||| ||||| || ||||||||||||||||| ||||  |  |  | | ||       |     ||  | |  |   ||   |        |                                                                 
---------------------CCTGTTCGGAGTGGACTACGACAACATCGACATCGTCATCCACCCCCAGTCCATCATCCACTCCATGATCGAGACGCAGGACTCCTCCGTGCTGGCGCAGgtgggggcaggagtggctgggcggctgggggctgggtgttttgcggctggtggctggtgcctggtgaatggggtgggggaaggtccgtagacagagcatg

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S62_157V6.2 (Physcomitrella patens), 5'ss of exon 11
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatat--gagttgaatgcttcaacacacaactaacacagctagtcaaatacag----------------------------------------------------------------------------------------------------
 || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | |||||||||||||       |||  |    |  |          | ||   | ||  ||||                                                                                                       
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgt-gaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaattgctgacttctgggatgatgtctgtatcctctgttttatag

upper sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 5'ss of exon 11
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgcttcaacacacaactaacacagctagtcaaatacag------------------------------------------------------------------------------------------------------
 || || |||||||| || ||| | || |||||||| || ||||| ||||| |||||| | ||||||||||| ||||| || |||||| | ||||| |||||  |||    | |   |  ||    |   ||  |  | | |  ||  |                                                                                                          
GGAAGTGATTGAAGCCCATTATCTCTTCGGAGCTGATTACGATGATATTGATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtt-tatctcataatcaccgcagagaaattctttccaatcaaaccatgtttgaaagagttgttatttgattacagactggagtaacctttaacatttttcgatttggtcaaatggtttctgacttttgagatgatggatgtgacttgtctgatag

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|169068926|gb|FE477267.1|FE477267
EST:     ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169096850|gb|FE498631.1|FE498631
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169096851|gb|FE498632.1|FE498632
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169034723|gb|FE443431.1|FE443431
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169114145|gb|FE516824.1|FE516824
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169106994|gb|FE505965.1|FE505965
EST:     ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169114144|gb|FE516823.1|FE516823
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169025379|gb|FE435993.1|FE435993
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169076204|gb|FE485234.1|FE485234
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
EST: gi|169081281|gb|FE488764.1|FE488764
EST:     ACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAG                         GATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT
genomic: ACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATT

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: 34 (upstream exon), 34 (downstream exon)
Score: 26

CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATTCTTTACACACTCTCTTGGCCGGATAGAGTTCCATGCTCAGAAATCACCT




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