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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG

Basic information

species Zea mays
transcript GRMZM2G082181_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g47530.1 (Oryza sativa), 3'ss of exon 5
gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatca--tttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG-----
||| |  || ||||| |     |   | || | | | |     |||| | |     | ||      |||| || ||||| |   | || || | |||| ||||||||| | |  || || |||  ||||||||||||||||||  |||||||||||||||||||||| || ||||||||||  ||   | | || |||||||  |||||| | || ||||| ||     
gtacttgtctttccaagaaccatacgagttatcaatgt-----tttgtcctaataaagaagctgcttttccttgatgtttttgtgata-ttgtggatatctgatagcatcgtt-ctcccgccaacacagATGGGCATTGCTTCCATTGTTCACCTCTATGTGTTCCCTGCGAAGCCCTATGAGCTGCAAGCCAACCAGTCACCAGGAAACGTCTCAGTACTCGGGGATT

upper sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 5
gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG-----
                  ||||    |||| ||||| ||    ||| | |||   | |  |    ||||        ||  ||  |   ||| |    | | ||||   ||  ||| || || ||||||||||||||||||  | |||||||| |||||||| ||||| ||||| ||||  |   |     | |  |     ||||   |||| || || ||     
----------------catgttcagcacttcttattttcatgttttacattt---ttatgactgcttca-------gataaggggaagaataaa-gtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGTGTTTCAGTTCTCGGAGATT

upper sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 5
gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG-----
                   |||    |||| ||||| ||    ||| | |||   | |  |    ||||        ||  ||  |   ||| |    | | ||||   ||  ||| || || ||||||||||||||||||  | |||||||| |||||||| ||||| ||||| ||||  |   |     | |  |     |||| | |||| || |||||     
----------------cacgttcagcacttcttattttcatgttttacattt---ttatgactgcttca-------gataaggggaagaataaa-gtttaacagcaatttgtattcatcaagcacagATGGGCATTGCTTCCATAGTTCACCTGTATGTGTTTCCAGCAAAGCCTTATGAGCGAATGGGAGACCGCTTTTCTGGAAGCGTTTCAGTTCTTGGAGATT

upper sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------gtattcatccttccagggtgt-----ttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG-----
                                                  ||  || |  ||   | |||      ||||   |  ||  |  ||||           ||    | || | |  ||    || | |   ||  |  |    | | | |    | ||   |  |||||  |||||||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||  ||  |     | |  |     |||  | |||| || |||||     
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca----cttgtgctggtccagtgcagATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGGTGACT

upper sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G38360.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------gtattcatccttccagggtgt-----ttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG
                                                  ||  || |  ||   | |||      ||||   |  ||  |  ||||           ||    | || | |  ||    || | |   ||  |  |    | | | |    | ||   |  |||||  |||||||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||  ||  |     | |  |     |||  | |||| || |||||
gtaaatgtcttctgttgttaccaattcctgcaaaaggttaaacattatgtgtgatctttgtttacgagtgcaaaactttttcttcattgcttcctattaacaagcagtctatggagtcgtctgttttcctttctttaaataaattaaagctcttaaca----cttgtgctggtccagTGCAGATGGGTATTGCTTCCGTTGTTCACCTGTATGTATTCCCAGCAAAGCCTTATGGTCTAATGGGAGACCGCTTTACTGGATCCGTTTCAGTTCTTGG

upper sequence: GRMZM2G082181_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 7
gtattcatccttccagggtgtttttaactttttattctctatctttgcctttgcttaaaaatcatttcattcatgttatgtggcta-gttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG-----
                       | ||||  ||||  | |  || | |    |||  |||||  | |   | |||| || |   ||    |   |    | | ||   ||||  ||| ||||| |||||||||||| |||||| |||||||||| ||||| ||||| |||||||| ||||  ||  |     | | || |   ||||   |||| || |||||     
-----------------------tgaactccttatcttatgcctatac----gctgcaaaatt-tattggtaatgtcatcttcatacaaaactaaagtttaacaggttcatgtattcatccagcacagATGGGCATCGCTTCAATTGTTCACCTGTATGTATTCCCTGCCAAGCCTTATGAGCTAATGGGAGACCGGTTATCTGGAAGTGTTTCGGTTCTTGGAGACT

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: 40 (upstream exon), 47 (downstream exon)
Score: 21

GGTGATTGCAATAATGTATGCTTTGGGCCTTCTTAGAAGCCCTTTAGCCCAGAGCTTGGAGTTAAAATCAAGCATTCAAGATTTCATTATTTGCATAGAGgtattcatcc ... cttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 15

GGTGATTGCAATAATGTATGCTTTGGGCCTTCTTAGAAGCCCTTTAGCCCAGAGCTTGGAGTTAAAATCAAGCATTCAAGATTTCATTATTTGCATAGAGgtattcatcc ... cttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 27

GGTGATTGCAATAATGTATGCTTTGGGCCTTCTTAGAAGCCCTTTAGCCCAGAGCTTGGAGTTAAAATCAAGCATTCAAGATTTCATTATTTGCATAGAGgtattcatcc ... cttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 24

GGTGATTGCAATAATGTATGCTTTGGGCCTTCTTAGAAGCCCTTTAGCCCAGAGCTTGGAGTTAAAATCAAGCATTCAAGATTTCATTATTTGCATAGAGgtattcatcc ... cttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcatgttatgtggctagttatagatacctgatagcaccatggcttcctccagGACAGATGGGCATTGCTTCAGTTGTTCACCTCTATGTGTTCCCAGCCAAGCCCTATGCACTCTTAACTAATCAGTCACACGGAAACATTTCTGTACTTGG
                            acctgat  putative branch site (score: 24)
                                             cttcctcc  putative PPT
                    ttatagata  TA-rich tract