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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT

Basic information

species Zea mays
transcript GRMZM5G889923_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 5
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtag-cttcttgtgcctgaacattctgatgtggtgtt--gtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
    ||| || ||    |   |   |||||  | || ||||  ||||||    || | | |    ||| |  ||| ||||| |  |||| ||     ||  |||| ||||||||||| ||  | |||||||||||||| ||||||||||||||||||||||||||
--gtatactcttta-attacttcaaatctgc-cgaataaataccatgataattttatcgaccaactgttctcgaaaattctaaaatggtctttgcctatgaagGTGTTTCAAAGTGCAGCTTTGTTTGATTCTCTCACGGTTCGTGAAAATGTTGGATTCCTTTT

upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 4
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
                 |  ||| ||   ||| || | |||    | |||    | | | ||     |    ||| |  |  | |     ||| | | |||| || |||||||| ||||| ||||||||| | || ||||||||||||||||| || || ||
----------------gtaagtttcaga-gtattatgcaatatactaattcttattttgttttcaacgt---aacttattttttttaatctgtaa-atagGTTTTCCAAAGTGCAGCACTCTTTGATTCTTTGACTGTTCGTGAAAATGTTGGTTTTCTCTT

upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 4
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacat-tctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
               | |  ||| ||   ||| || | |||    | |||     ||  | | ||     | |   | | | || |     ||| | |||||| || |||||||||||||| ||||||||| | || ||||||||||||||||| || || | 
---------------ggtaagtttcaga-gtaatatgcaatatgctaattcttaggttacgttttaattgtaattttattttatttttatctgtaa-acaGGTTTTCCAAAGTGCTGCACTCTTTGATTCTTTGACTGTTCGTGAAAATGTTGGTTTTCTCT-

upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagctt--cttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
                    || |   |||| ||  || |||  ||   |     || | |    ||||  || ||     |  |||  |  |||   |||||| ||||| ||||| || || |||||||| ||  ||||||||||||||||||| || ||  |
--------------------gtaggtgctgttctg-gagatg-tatttctcataagtcgttgagtttgtatctaaatggctttttgtttt-ctgtctcacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT

upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
||| |      ||   ||||      ||| | ||     | |  || || |   |      || |||   |     ||||       | || ||| |||||||||||| ||||||||||||||||||||| | || ||||||||||||||||| ||||||||
gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttcta----atcatgtaattctgttttctt-----ctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT

upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ30431 (Selaginella moellendorffii), 3'ss of exon 3
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
                                        |  | | | |    | | || | |   | | |   ||| |    |   |  |   | ||||| |||||||| || || || |||||||| ||||||||||| |||||||| |||||  |  |
---------------------------------------gtaacgt-actgaactat-gcctttaccgtccgtgtattatcggcttacga-gctttgcagGTTTTTCAAAGCGCAGCGCTGTTTGATTCGCTCACAGTTCGAGAAAATGTCGGATTTATGCT

upper sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ22908 (Selaginella moellendorffii), 3'ss of exon 3
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
                                        |  |||  |   ||    |  | |   ||| |   ||| |    |   |  |   | ||||| |||||||| || || || |||||||| ||||||||||| |||||||| |||||  |  |
---------------------------------------gtaacatactgaacta--cgtctttaccgcccgtgtattatcggcttacga-gctttgcagGTTTTTCAAAGCGCAGCGCTGTTTGATTCGCTCACAGTTCGAGAAAATGTCGGATTTATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttccttgtagcttcttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
                               ttctgat  putative branch site (score: 3)