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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatttacatgagcatcaaattcatttaaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA

Basic information

species Zea mays
transcript GRMZM2G374973_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
gtaatg-atttacatgagcatcaaattcatttaaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
|||| | |||||  |   | ||   || |  |    |  | ||  ||  |   | ||  ||| |        | |  |||||| ||||||| || |||||||||||||| |||||||||||||| |||||||| ||||| ||||| |||||||||||||| || || |||||||| |||||||||||||
gtaacggatttatctacacttc---tttagctccaatcccatttcttgcgcagtgacaatcctt-------aacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA

upper sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
--------------------gtaatgatttacatgagcatcaaattcatttaaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
                     | || | || |||   | |||| ||||| ||   || ||  | |       | |  ||    |    ||||| | |      ||||||| || ||||||||||||||||| ||||| ||||| || || || || || |||||||||||||| ||||| || ||  | ||  | ||  | ||||| |
atgatcaaatatttgagcctatcataacttgcat---cttcaatttcatgtacatttcctcaaataggaggctaatacttgaat----atgat-tttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA

upper sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
----gtaatgatttacatgagcat-caaattcatt--------taaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
     |  ||  |||    |  |  ||||   | |        || | || | |   | ||   |  ||      || | ||  || ||   |   ||||||| || ||||| ||||||||||||||||| ||||| |||||  |||| ||  |||| |||||||||||||| || || ||||| || ||| | |||||  
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcc-tactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG

upper sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ04955 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgatttacatgagcatcaaattcatttaaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
                                || | ||   |  | | ||   |     |  ||| || | ||| ||     | ||| ||||||| || || |||||||||||||||||||| || ||||| || |||||  | | |||||||||||| |||  |  ||| || |  |||| | |  
------------------------------gtagttgtcagaaagtgatttgacatggagcaatttcaacg-tatttg----ttacagGTCCGGTTCGTAGTCATGGGAAACATGTTTTGCACGGACTTGAGGATACACCGCCGATATGATTTGAAAGGATCGCTTCAAGGACGTTGCACTGGCGAGG

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), 10 (downstream exon)
Score: 1

AATGCTTCCAAAGTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACCAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTAGTGGCCAAATGgtaatgattt ... caaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 16

AATGCTTCCAAAGTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACCAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTAGTGGCCAAATGgtaatgattt ... caaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA


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

AATGCTTCCAAAGTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACCAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTAGTGGCCAAATGgtaatgattt ... caaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 9

AATGCTTCCAAAGTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACCAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTAGTGGCCAAATGgtaatgattt ... caaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
                              ttttaat  putative branch site (score: 9)
      tttagtttagttttta  TA-rich tract