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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaaccttttccttttccagctctgattatttctattgtgactgtgacag

Basic information

species Selaginella moellendorffii
transcript EFJ15673
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagag----aaaccttttccttttccagctctgattatttctattgtgactg--tgacag----------------
| ||||| ||||| ||||||||||| || ||||||||||| |||||||| || || ||  | || || || || ||  | || || || ||||| ||||||||||       ||| || | ||| || |    |||   ||||||||     ||  | |  |                
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttcttctctattgttgacattttctattcaacttgacttatggaaatctttctctgtag

upper sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 2
TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagag----aaaccttttccttttccagctctgattatttctattgtgactgtgacag-----------------------
| ||||| ||||| ||||||||||| || ||||||||||| |||||||| || || ||  | ||||| || || ||  ||||||| || ||||| ||||||| ||        || |  |||||||   | | || |   |||| |||    |    |                         
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGCTTGGGATCTGGCATTTCTCTGTTCATTGCTACCAATATCTGgtaagcatcttggacttaatccttttattgatgtgctg--ttctgttgcacttaaagcttataataagaattctttcatgtag

upper sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 2
TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgag------agaaaccttttccttttccagctctgattatttctattg---tgactgtgacag-----------------------------------
| ||||| ||||||||||||||||| || || ||||||||||| ||||| || || ||  | ||||| || |||||  ||||||| || || || ||||||| ||      |    ||| ||   ||  |  |     ||    |  ||    | ||| |                                        
TTTTCTTTGCTGGTATCATTGTCATCTGTCTAGATGAACTCCTACAGAAAGGCTATGGTTTGGGATCTGGTATCTCTCTGTTCATTGCTACGAATATCTGgtaagcatattaagggcctgtttggttcactacctcagttgccacactttgcctaacttttctgcctaaggttagttattcaattcgaactactaacctt

upper sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G073498_T03 (Zea mays), 5'ss of exon 3
--------------------------TCTTCTTCGCT-----GGTATCATTGTCATTTG-CCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATC-GGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaaccttttccttttccagctctgattatttctattgtgactgtgacag
                          || |  | |||     || | |  || ||| || ||||  || | |       |  | |  |   |||||| | ||||||    |  |   ||  |  || | | |  |    |  | | ||  | | |       |||   | || |    |  |       
GAATGGTGCACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGCAGTgtaagccaacttggaacagggaatgctatcctcattatacttcagcttttctttgctggcatcattgtcatctgtctggatgaacttctccagaaaggtt-------

upper sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 5'ss of exon 3
TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaaccttttccttttccagctctgattatttctattgtgactgtgacag-----------------------------------------------------------------------------------------------------------------------
|||  || |||||||||||||| || ||  | |||||||| || ||||| ||||| |||||||| || ||||| ||  | |||||||| || || ||||||||||       || |  || |     | |  |||||  | || | | | |||                                                                                                                          
TCTGTTTTGCTGGTATCATTGTGATATGTTTAGATGAACTTCTGCAGAAAGGATATGGGCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgtgagcatctggttctttttctgggattttttttattaat-ttatcattttgaacatggaatatttgaagaagctttactatctagcagccagcgtctggtgaatgtggtctcatttctgggttgaccattaactctactgtcaaatagtgacaattgttttgatcaattggcag

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|169067827|gb|FE473398.1|FE473398
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|169044323|gb|FE453261.1|FE453261
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTNTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|169100434|gb|FE501322.1|FE501322
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGAACATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|169067826|gb|FE473397.1|FE473397
EST:     ACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: ACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|169043639|gb|FE452694.1|FE452694
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|70669535|gb|DN838112.1|DN838112
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|169043638|gb|FE452693.1|FE452693
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
EST: gi|70669900|gb|DN838477.1|DN838477
EST:     GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTG                         TGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG
genomic: GGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCG

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), 34 (downstream exon)
Score: 23

TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagagaaa ... actgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTTGAGGGAGCTATCATTGCTCTCTTCCACCTCTTGATC




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