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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttccatttgcgatgttgggcgatggcgatctcgatgttggtactcacaattttgctcctcccag

Basic information

species Selaginella moellendorffii
transcript EFJ23432
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g42150.1 (Oryza sativa), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttccatttgcgatgttgggcgatggcgatctcga-tgttggtactcacaattttgctcctcccag
|| |||| ||||||||| ||   |||||  |||  ||||| ||||| ||||||||||||||||||||||||| | | ||| ||  |||||||||||||||||| |   |   | |||  | | |   |  |     | |   |  |   | ||   |  | |  ||||      |  | |  | |   |||
TCGTCACGTACGAGGACATCCTCCCCGACGTCCTCCGCATCGCCAACGGCGACACCTCGCCCATCCTCTCCGGCAAGCCCGTCAGCGAGTTCCTCACCAGgtaggtgtgctctactcc-tgcatgcgtgtacacatggtcgagcacttcgccggcgtgaactaatggtgtggtgatgtataatgcgtgcag

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g55940.1 (Oryza sativa), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaag-aaagaaattctcgatccttctttccatttgcgatgttgggcgat--ggcgatctcgatgttggt---actcacaattttgctcctcccag------------------------------------------------------------------------
|| |||||||||||||||||   || |||||| | ||||| ||||| ||||||  |||   |||| ||||| |||| |||||| ||||||||||||||||||  | | || | | || | |    |   | ||||    | |      ||  |||  |     ||  ||     |||     ||  ||||  | |                                                                         
TCGTCACCTACGAGGACCTCCGCCCGGAGATCGAGCGCATCGCCAACGGCGACCGCTCCAACATCATCTCCTCCCACCCCATCACCGAGTTCCTCACCAGgtgtgtatagtagtgctagctaacccaaacaatttcttttttcaattaatccggcctttcatttgccggctcggctccgccattgactccaactaattgtttgattagtttttggtcgttgcttggttgatcgttcttgcttactaattggcgtgcgtgtgcatccag

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g37960.1 (Oryza sativa), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaaga--aatt--------ctcgatccttctttccatttgcgatgttgggcgatggcgatctcgatgttggtactcacaatt-ttgctcctcccag
|| |||||||||||||||||   || |||||| | ||||  ||||| ||||||  ||||  |||| ||||| |||| |||||| ||||||||||||||||||  | |  |  |  |        |   || | | |||| |||     ||     |  | ||   ||||     |  |   ||      |  |  |   | 
TCGTCACCTACGAGGACCTCCGCCCGGAGATCGAGCGCACCGCCAACGGCGACCGCTCGAACATCATCTCCTCCCACCCCATCACCGAGTTCCTCACCAGgtgtgtagtactagctaacccaaacaaaattcctttttcaattaatcctgcctttcatttgccggctcggctccgccatctactccaactaattgtttga-

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g57610.1 (Oryza sativa), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttccatttgcgatgttgggcgatggcgatctcgatgttggtactcacaattttgctcctcccag-----------------------------------------------------
|| |||| ||||||| |||| |||| || ||||  ||||| ||||| |||||||||||||| ||| ||||||   | || |||||||| |||||||| |||||    | ||  | |         | | |||         || | |   ||   | || || ||     || ||  | |     |  |                                                      
TCGTCACATACGAGGGCCTCCAGCCAGACATCCTCCGCATCGCCAACGGCGACACCTCGCCGATCTTCTCCGGGAAGCCTATCTCCGAATTCCTCACGAGgtatagcacaatatataacgtgacatgttcatgcttccccgtgtgtgtacgcacgcacgctgctg-cgtgcaaaacctagaaagacgtacgagttcatatctgtacagatcttcatgcaatggaatttcatcatgtccaccag

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G068701_T01 (Zea mays), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttc---tttccatttgcgatgttgggcgatggcgatctcgatgttggtactca--caattttgctcctcccag--
|| ||||||||||||||||  ||||||| ||||| ||||| ||||| || |||  |||||||||||||||||| ||||||||||||||||||||||||||||| |       || |   || ||    ||||    || | |    |  || | ||   |  ||  | | | ||   |  ||    ||||       
TCGTCACCTACGAGGACCTGCAGCCCGACATCCAGCGCATCGCCAACGGGGACCGCTCGCCCATCCTCTCCGCGCATCCCATCTCCGAGTTCCTCACCAGgtacgcgcattttttttattcattgggatttctgcctgtgttaggtgttgacgtcgccttgtataattggattcgatcgcttccattcctaatgaag

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G061515_T01 (Zea mays), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttccat--ttgcgatgttgggcgatggcgatctcgatgttggtactcacaattttgctcctcccag--------------------------------
|| |||||||||||| |||| |||| || || |  ||||||||||| |||||  ||||||| |||||||| | | | |||||||||||||||||||| |||||  | |   || |   |       |  ||    || ||||    |||   | |   || |  ||   ||  |||      |   | |                                   
TCGTCACCTACGAGGGCCTCCAGCCGGACATACTCCGCATTGCCAACGGCGATGCCTCGCCGATCCTCTCAGGCAAACCCATCTCCGAGTTCCTCACGAGgtagtatattcatccctcacgtacgatcacaacgctgtgatgc-atgcggctgtggaatcaaaattta-acggacatgggaacatgtactgatttataactgaggatgtttgtgtgtgaaccag

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G366873_T01 (Zea mays), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttcc------atttgcgatgt---tgggcg-atggcgatctcg-atgttggtactcacaattttgctcctcccag------------------------------
|| |||||||||||||| ||  ||||||  | |  ||||| ||||| || ||||| |||||||||||||||| | | ||||||  ||||||||||||||||| ||  ||     ||    | | |  |         | ||   |||   |  | | ||| |||  ||| | |   |     | | |  |  |  |    |                              
TCGTCACCTACGAGGACATCCTGCCCGACGTGCTGCGCATCGCCAACGGGGACACGTCGCCCATCCTCTCCGGCAAGCCCATCCGCGAGTTCCTCACCAGgtgagccagcctgcctgccccgtgccgtgtgaggaggtctgtagtgtgtgtatgtgcatgtcgacgtcgcacgcgcgcgtgaagagtgatagtaataatggccgtacccgtacgtgcgatgatggtggcag

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA02G13910.1 (Glycine max), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttccatttgcg-atgttgggcgatggcgatctcgatgttggtactcacaattttgctcctcccag------------
|||| |||||||||||| || |||| ||||| || ||||| ||||||||||||  ||| |||||||| ||||| || |||||||||||||| ||||||||||||  |     |||   |  |     || ||||    ||    |     |   |  |  |  |    |     || |||     |   |             
TCATAACCTACGAGGACGTCCAGCCGGAGATTCAGCGCATCGCCAATGGCGACCGCTCCCCCATCCTGTCCGCTCACCCCATCTCCGAGTTTCTCACCAGgtaattacttgcttc--aacacaatactcaatttaaatataccagaaagagatcaattt-acatcaacatgagtaactttttcagttaaataaaattaatgac

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G18080.1 (Glycine max), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatccttctttccatttgcgatgttgggcgatggcgatctcgatgttggtactcac-aattttgctcctcccag-------------
|| |  | ||||| ||  |  |||  || |||||||||||||| ||||| |||  ||| || ||||| | ||| ||||| || |||||||| ||||||||||| |       || ||  || || |||   |||      ||   |  | |  |  |  || ||  || | || |||||   |      |              
TCGTTTCATACGATGATTTGAAGCATGATATCCAACGCATTGCTAATGGTGACCGCTCTCCTATCCTATGCGCTCATCCAATTTCCGAGTTTCTCACCAGgtacgtttt---ttttctttcttttttttttttttttgcattacacagtcgtaaaatgtat-ttaataatgaccaatttaaattggagtaagcgagcaattttt

upper sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT2G14960.1 (Arabidopsis thaliana), 5'ss of exon 1
TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaagaaattctcgatcct---tctttccatttgcgat--gttgggcgatggcgatctcgatgttggta-ctcacaattttgctcctcccag
|||| || ||||| || ||| |||| ||||| |||||||||||  |||| |||  ||| |||||| | || |||||||||||||| ||||||||||| ||||  |      || ||   | ||   ||||| | ||  ||||   |    | ||    |||   |      || |||  ||      |  |||   
TCATTACATACGAAGATCTCCAGCCAGAGATTCAACGCATTGCTGATGGAGACCGCTCTCCCATCTTATCTGCCCATCCCATCTCTGAGTTCCTCACTAGgtttgttcaccatactttgttctctatctttactttaccgattactaaatcaatcaaaatccataaaccaataactcctaaaaacatttttccag-

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: 11 (upstream exon), 25 (downstream exon)
Score: 1

TCATCACCTACGAGGACCTCGAGCCCGAGATCCAACGCATTGCCAATGGCGACACCTCGCCCATCCTCTCCGCCCATCCCATCTCCGAGTTCCTCACCAGgtaagaaaga ... ctcctcccagCTCGGGAACGTCGGCTGGCCAGAGGAAACTCATGCCCACCATCTCGGAAGAATTCGAGCGCCGCTGCCTGCTCTACAGCCTCCTCATGCCCGTGATGAAC




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