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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgtcgtcgatccaaatccaacgctgttgctgtgccgtcctctgttctctgttcctaaccctttttttttctttcttcttttacgacgaccggccggtgcag

Basic information

species Zea mays
transcript GRMZM2G123886_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123886_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 5'ss of exon 3
GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgtcgtcgatccaaatccaacgctgttgctgtgccgtcctctgttctctgttcctaaccctttttttttctttcttcttttacgacgaccggccggtgcag---------------------------------
|||||||||||| || |||||||| ||||| ||||| ||||||||||| ||||||||||| || || |||||||||| |||||| || || ||||| |||||| ||  || |  | |     |||| ||||      |  |  |||  |||    | |  ||   ||       |   | ||    |     |  | ||                                  
GGAGAACTTCAATGATGTCTACATTGTCTATGAGCTCATGGACACTGATCTTCACCACCTTCTTCGATCAAACCAGCCACTAACAGATGATCACTGTCAGgtc-tcactcta--ttcttgtttgtttctgtattaaaccat-ctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcag

upper sequence: GRMZM2G123886_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S149_39V6.2 (Physcomitrella patens), 5'ss of exon 4
GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgtcgtcg-atccaaatccaac--gctgttgctgtgccgtcctctgttctctgttcctaaccctttttttttctttcttcttttacgacgaccggccggtgcag
|||||| ||||||||||| ||||| || |||||| ||||||| || ||||| |||||  || | || ||||| ||    || || || |||||||| ||||| |    ||  |  |  ||   |   ||   ||   ||  |   |||| || |  | |||    | |  |     |  | | |   | |     |  |    
GGAGAATTTCAACGACGTGTACATTGTATACGAGTTGATGGATACGGACCTACACCAGATCATTCGTTCAAATCAAGCTCTCACAGAAGACCACTGTCAGgttgagacatatacctttaattagagattttggttgtgttttaacttctatgcttgtgacctgagtatcgttaagatgatgtaaaagctagaaaactcta---

upper sequence: GRMZM2G123886_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S59_325V6.1 (Physcomitrella patens), 5'ss of exon 2
GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgt-cgtcgatccaaatccaacgctgttgctgtgccgtcctctgttctctgttcctaaccctttttttttctttct----tcttttacgacgaccggc--cggtgcag---------------------------
||| |||||||||||||| ||||| || || |||||||||||||| || ||||||||  || | ||    || ||||  || || || ||||||||||||||  | |      | |       | ||  | |    |  | || |  |  ||| |   |  |||| ||   | ||    | |||   |  ||   |   | ||| ||                           
GGAAAACTTCAACGACGTGTACATTGTATATGAGCTGATGGACACGGATCTTCACCAGATCATTCGTAGCAATCAGCCGCTGACAGAGGACCACTGCCAGgtgtgactgattgattttttttttttttttttttttttttttgctaccgtttcttcgtcgattttcttcactactgttgtttttcttgttgatgtgtggcagtggagtttgagatactgtgttactttgtgcag

upper sequence: GRMZM2G123886_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ04892 (Selaginella moellendorffii), 5'ss of exon 3
GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgtcgtcgatccaaatccaacgctgttgctgtgccgtcctctgttctctgttcctaaccctttttttttctttcttcttttacgacgaccggccggtgcag
|||  | ||||||||||| || ||||| |||||||| |||||||| || || |||||  || | || || |||||||| || || ||||||||||| |||||                   |      ||||   ||| ||      || | |  |  |||        |    |   || ||    | |          
GGACGAGTTCAACGACGTGTATATCGTGTACGAGCTCATGGACACGGATCTACACCAGATCATCCGCTCCAACCAGCAGCTCACGGACGACCACTGTCAGgtt------------------cctcccttgtgttttcccctcgctcttgctacctaggcttgacggacgtggtgtggcttgcgggcgcag----------

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 2 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 13

GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgtcgtcgatc ... gccggtgcagTACTTCGTGTACCAGCTGCTCCGCGGGCTCAAGTACGTGCACTCGGCGAACGTCCTGCACAGGGACCTGAGGCCGAGCAACATGCTGCTGAACGCCAAGT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 7

GGAGAACTTCAACGACGTCTACATCGTCTACGAGCTGATGGACACTGACCTTCACCACCTCCTACGGTCAAACCAGCAACTAACCGACGACCACTGCCAGgtcgtcgatc ... gccggtgcagTACTTCGTGTACCAGCTGCTCCGCGGGCTCAAGTACGTGCACTCGGCGAACGTCCTGCACAGGGACCTGAGGCCGAGCAACATGCTGCTGAACGCCAAGT




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