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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctctcagtgcaatgcatccttctctaatccctccatgcag

Basic information

species Selaginella moellendorffii
transcript EFJ18240
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 5'ss of exon 8
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgt-------------ttgctctctcagtgcaatg--catccttctcta-atccctccatgcag-------------------------------------
  ||| || ||  | ||||| || |||||||| ||||||||||| || |||||||  ||||| ||||| ||||||||||| || |||||             || | ||||   ||||||   ||| | | |||| | |    ||   |                                      
AGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAGgtaagtattccttgatttcactcttgttgcaatagccattcatttctatacctaatcaaaaaatacgtaaggtttccagtagttattttcgtctgtttct

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 7
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctctcagtgcaatgcatccttctctaatccctccatgcag---------------------------------------------------------
|| || || ||  | ||||| || |||||||| |||||||||||||| |||||||  ||||| || || |||||||| || || |||||| |   |||   |  | ||  |    ||||  |      |   |                                                          
GCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAGgttagtgttctttata-agtgattttgactcttgttttgatacaaaatgtctttttctttttacaaaaaaaggctaatctggttatccccttttttctgcatag

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttg--ctctctcagtgcaatgcatccttctctaatccctccatgcag-------------------------------------------------------------------------
|  || || || || |||||||| |||||||| ||||||||||| || |||||||  || || || || ||||||||||| || |||||  |  |||| |||     |  | |  ||   |||| ||    | |||                                                                         
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaacctttttttgttaataccattgt-cagtcactcagttagttggttccatttttctcatcttgatgcttcagctgatctggctttgtttggttatgtacag

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA14G21190.1 (Glycine max), 5'ss of exon 3
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctctcagtgcaatgcatccttctctaatccctccatgcag------------------------------------------------------
|| || || || || |||||||| |||||||| ||||||||||| |||||||||| |||||| || || ||||||||||| || ||||||  |  | | | || |||   |   | | |  |  || | ||                                                         
GCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttaacatttt-aatgaaataattttatttttcctatcttcgtgtgaagtttaaatgtttaatactcccttgattgcgaaactgtagactttcttgtttaa

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 8
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctctc---agtgcaatgcatccttct-ctaatccctccatgcag----------------------------------------------------------------------------------
|| || ||||| || |||||||| |||||||| |||||||| || |||||||||| |||||| || || ||||||||||| || |||||| | | | |    | || |||| |   ||||  |  ||  |   || |                                                                                   
GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttagtttttttgctaatgaaatggagatttctgtttgtctttgtgtgaattttaattgtgtacttactatgatatcagataaaaaaatgtaataaatctattcctaatattgtcattcaaattattttgcag

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA06G08620.3 (Glycine max), 5'ss of exon 8
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtt---tgctctctcagtgcaatgcatccttct-ctaatccctccatgcag-----------------------------------------------------------------------------------
|| || ||||| || |||||||| |||||||| ||||||||||| |||||||| | |||||| || || ||||||||||| || ||||||   |  | |   | || |||| |   ||||  |  ||  |   || |                                                                                    
GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttaagttttttgctaatgaaatggagatttctgtttgtctttgtgtgaattttaattgtatatttactatgatatcagataagaaaaatgtaataaatctattcctaatattgtcattcaaattattttgcag

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctctcagtgcaatg---catccttctctaatccctccatgcag-------------------------------------------------------------------------------------------
|| || || || || ||||| || |||||||| ||||||||||| ||||||||||  ||||| |||||||| |||||||| || |||||  | | ||   ||  | ||    ||   ||    ||       |                                                                                               
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag

upper sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: PP1S47_5V6.2 (Physcomitrella patens), 5'ss of exon 8
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgt-ttgctctctcagtgcaatgcatccttctctaatccctccatgcag----------------------------------------------------
|| || || ||| |||| |||||||||||||| |||||||| ||||| ||||| | ||| || ||||| || |||||||||||||||||  |   | |    |    | | || |        |    || || |                                                    
GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaagctgtgttatgagagagctacttgacaacaatggaatgagacatgtttcgtgagct

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|169059125|gb|FE468270.1|FE468270
EST:     TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG                         CTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
genomic: TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
EST: gi|169110321|gb|FE512080.1|FE512080
EST:     TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG                         CTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
genomic: TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
EST: gi|169110322|gb|FE512081.1|FE512081
EST:     TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG                         CTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
genomic: TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
EST: gi|169074072|gb|FE481732.1|FE481732
EST:     TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG                         CTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
genomic: TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
EST: gi|169059126|gb|FE468271.1|FE468271
EST:     TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG                         CTAATCTTCCCGACTGGCTCTTCGAGCNAACCGTTCTCTATGCTGGGTCTC
genomic: TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
EST: gi|169074073|gb|FE481733.1|FE481733
EST:     TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG                         CTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC
genomic: TCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTC

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: 27 (upstream exon), 35 (downstream exon)
Score: 12

GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttgctctc ... ctccatgcagCTAATCTTCCCGACTGGCTCTTCGAGCAAACCGTTCTCTATGCTGGGTCTCGGCGACATAGTAATCCCAG




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