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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag

Basic information

species Zea mays
transcript GRMZM2G354532_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 24
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcatt-cagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag
|||| || |||||||||||||| || ||||| || ||||||||||| |||||||| ||||| |||||||| |||||||| |||||||||||||| ||||||| |  | | |  | ||    ||||  |||  ||   |     ||  ||||  | ||| | | |   |  | | |   ||||   | || | |                                                                                       
ATGGATTACGCACTAAAGATAAAGAACGTGTACTGGTTCTTGGTGCCACAAATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagctataaccttgtgttggggttgggataatgaa--aaattgctgtt-tgttgatttctaaccatttggtcgttaattactactgtag---------------------------------------------------------------------------------------

upper sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 20
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag
|||| ||| | || |||||||| |||||| | |||||||||| ||||||||||||||||||||| || || |||||||| ||||||||  | || || |||||||  | |||   ||   ||        ||| |   ||  ||  | ||  |||     || |  | ||| | ||    ||||    ||||   |  |||| | | |                                                                       
ATGGTTTGAGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCTGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcgttatgtttgatg--------ttaacttcttttatttc-gtgttttacaaatgagatctatgctaat----tcgtgttctttgttgaaaaatattgtag-----------------------------------------------------------------------

upper sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 20
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag
|||| ||||| || |||||||| |||||| | ||||||||||  |||||||||||||||||||| || || |||||||| ||||||||  | || || |||||||  |  ||   ||   ||        | | |   ||  ||  | ||  ||      || |  | ||| | || |    |||  || | |  |  ||| ||                                                                           
ATGGTTTGCGAACAAAAGATAAAGAGCGTATACTTGTTCTTGCGGCTACAAATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaac-tcattatgtttgatg--------tcagcttcttttatttc-gtgtttcacaaatgagatctatgctaatttg--tgttctttcttgaaaaaaattgtag-------------------------------------------------------------------------

upper sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 23
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag
| ||  || | || || || ||||| ||||| || |||||||  || |||||||||||||||||||| ||||||||||| ||||| ||||| || |  |||||| |  | | |   |   | |   |||| ||   || |      ||||    |||   ||| |   |    | | |  |  | |||| ||                                                                                       
ACGGTCTGAGGACAAATGAAAAGGAACGTGTTCTGGTTCTTGCAGCCACAAATAGACCTTTTGACCTTGACGAGGCTGTCATTAGAAGGTTGCCTCATAGgtaatttatatatagcttccttg--ttggacta---agcttt----ctgtcaaattgacatgtcg-taacaagtttttggtattggcttctgcag------------------------------------------------------------------------------------

upper sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 24
ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaaatcgctgctgctggttccatattcatcaccatcttactcattgtttcag
|||| |||||||| |||||||  ||  | || || || ||||  || |||||||||||||||||||| || |||||||| ||||| ||||| || || ||||||    |   | |  || |  |  |||| || ||   |  ||  |   |   | |  || | |  |    || | |||| |||  | ||    ||                                                                                  
ATGGCTTGCGCACAAAAGATACCGAAAGGGTTCTGGTGCTTGCAGCCACAAATAGACCTTTTGACCTTGATGAGGCTGTTATTAGAAGGTTGCCGCGTAGgtaaggcatcactgagccattttg-ttggactatcctactttatttccacaaactgggact-tagttc----ttctgtaatggttcatcttttacag----------------------------------------------------------------------------------

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: 274

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAACAGAGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAACAGAGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAACAGAGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 266

ATGGGTTGCGCACTAAAGATAAGGAGCGTGTGCTTGTTCTTGGTGCTACAAATAGACCTTTTGACCTGGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAACAGAGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT