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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaatctttgtgtgtgtgtgtggggggggggggtcttaaccgcactatactattgtttattcatgtcattcctgctttctaatattgaatcctcttttcttacctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG

Basic information

species Zea mays
transcript GRMZM2G700148_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
gtaattaatctttgtgt----gtgtgtgtggggggggggggtctt--aaccgcactata--ctattgtttattcatgtcattcctgctttctaatat-tgaatcctc----------ttttcttac--ctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG
|||  |||| ||    |    || | |     |         |||  ||    | |      | || ||| |  |||||||   |   |  |  ||| ||||||||           || ||||    ||||||| ||| | |||||||||||||||||||| |||||| |||| |||||||||||||| ||||| || ||||| |||||| | || |  ||           
gtatataatattgaaatagtggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttctcagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG-----------

upper sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------gtaattaat-ctttgtgtgtgtgtgtggggggggggggtcttaaccgcactatactattgtttattcatgtcattcctgctttct---aatattgaatcctcttttcttacctc-----agTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG
                                                  ||||    | |    |        |         ||     ||| |  | || |  |    | |  ||  |  | ||||  | |    |||  | | |   |  |||  || |      |||| ||    ||||| || |||||||||||||| || ||||| || || |||||||||||||| || || ||||| ||| | || |  ||           
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaa--aatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG-----------

upper sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
-----------------------------------------gtaattaatctttgt-gtgtgtgtgtggggggggggggtcttaaccgcactatactattgt-------ttattcatgtcattcctgctttc-taatattgaatcctcttttcttacctc------agTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG
                                          | |||||  |     || | |   |       |             || || || |  |        | |  ||  |  | ||||  | |  |||  | | |   || |||  ||         |||| ||    ||||| || |||||||||||||| || ||||| || || |||||||||||||| || || ||||| ||| | || |  ||           
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG-----------

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: 48 (upstream exon), 48 (downstream exon)
Score: 103

CATTAGACGGAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAAGAAATTGTTGAGGAGTTGTTGCAGgtaattaatc ... cttacctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

CATTAGACGGAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAAGAAATTGTTGAGGAGTTGTTGCAGgtaattaatc ... cttacctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

CATTAGACGGAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAAGAAATTGTTGAGGAGTTGTTGCAGgtaattaatc ... cttacctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

CATTAGACGGAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAAGAAATTGTTGAGGAGTTGTTGCAGgtaattaatc ... cttacctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttattcatgtcattcctgctttctaatattgaatcctcttttcttacctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG
                                           ttcttac  putative branch site (score: 88)
                                    tcctcttttcttacct  CT-rich tract
                      tttctaatattgaat  TA-rich tract