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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcttattggcctgcctgcctgccctggatctaggcctcctgcttcgccggatcctcagatcacatctctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG

Basic information

species Zea mays
transcript GRMZM2G083546_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
-------------gtacgtgcttattggcctgcctgcctgccctg-gatctaggcctcctgcttcgccggatcctcagatcacatctctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG
              |  |  ||| ||   || | |    |||    ||   ||  ||| ||       | ||  ||   |      |    |  ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |
gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtacta--gtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG

upper sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------gtacgtgcttattggcctgcctg--cctgccctggatctaggcctcctgc-----ttcgccggatcctcagatc---acatctctccttg-----------cagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG
                                                                                   ||  ||| ||  ||   | |  |  |  |     |||||  |   || |      |  |   |||  |   ||    |   || |  ||            |||||||| ||||| ||||| || |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||| ||||| |||||||| || || |
gttttttgtttataattttgaatttcaatttgagtgcataatcgttggttccgtgatttcgtttaatatagtctgaacttttcgtttgtggtttctgatttacgagatctggtttcagatctgtgatacccgtggtagtgtgtttgatttttgaatttgtatggcttttttttttttttaatttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCG

upper sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------------------gtacgtgcttat-tggcctgcctgcctgccctggatct--aggcctcctgcttcg---ccggatcctcagatcacatctctcc---ttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG
                                                             ||   || || | ||  ||      |||     |||||  |||  ||  | || |    ||| |  | |  |    ||| |     ||  ||||||| || || || || || |||||||| || ||||| |||||||| || || |||||||||||| |||||||||| ||||| ||  | || |||||||
gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgtttttattttggtttttggttttctgttcttgagatctggttcagatctggaggtttcgcgattggatctcggttttttattttgtttctttttggtttttagATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGG

upper sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 1
lower sequence: EDO98081 (Chlamydomonas reinhardtii), 3'ss of exon 1
---------------gtacgtgcttattggcctgcctgcctgccctggatct----------aggcctcctgcttcgccggatcctcagatcacatctctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG-
                  |  | ||    ||| |  |||| | || |||             | | |   |||   ||  |    || || |    || ||||||||| |||||||||| |||  |  ||||||||| ||||||||||||||  | || ||  ||||| |||||||  ||||| ||| | |||| ||   | |||||  
gtaagttgcaggcatacgcaggattggacgccggggtgcccggccgggacggcaggtgggggaaggcagttgcggagcgagcgtgtctgaacggg-ctgtccttgcagGTGTGCTTCGATTGCCCCAACAAGAACCCGACCTGGGCCTCCGTGCCGTATGGAGTCTTCATCTGCCTGAACTGCGCGGGCATCCATCG-GTCTTTGGGAG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 373

GCAGCTAGCCATGGCGGCGGCGGCGGCGGCGGCGGCCTTCGATGCCTACACCGACAAGAACGCCATCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtacgtgctt ... ctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 373

GCAGCTAGCCATGGCGGCGGCGGCGGCGGCGGCGGCCTTCGATGCCTACACCGACAAGAACGCCATCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtacgtgctt ... ctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 224

GCAGCTAGCCATGGCGGCGGCGGCGGCGGCGGCGGCCTTCGATGCCTACACCGACAAGAACGCCATCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtacgtgctt ... ctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 407

GCAGCTAGCCATGGCGGCGGCGGCGGCGGCGGCGGCCTTCGATGCCTACACCGACAAGAACGCCATCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtacgtgctt ... ctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctggatctaggcctcctgcttcgccggatcctcagatcacatctctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG
                                     tcacatctctcctt  CT-rich tract