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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatttaagtatgttctttttacattttatgctagttcctgattcctgtagtgtctggatagttatttcttggctgatacattgctctgatgtacctgtaaagttcactttgcttccttgtactatgatctaaacagctaacatctttgtgagactaaaaattacattttaaattggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGACTGTGTGGGACCAAACTGTTGAGTATTGTGCATTTGCTTATCAGCAGTAT

Basic information

species Zea mays
transcript GRMZM5G824843_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 13
gtatatatttaagtatgttctttttacattttatgctagttcctgattcctgtagtgtctggatagttatttcttggctgatacattgctctgatgtacctgtaaagttcactttgcttccttgtactatgatctaaacagctaacat--ctttgtgagactaaa-aatta--cattttaaattggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGACTGTGTGGGACCAAACTGTTGAGTATTGTGCATTTGCTTATCAGCAGTAT
                                                                                      |  ||| |   |  ||      | |||         | | |  |||| |  || | |||  |  |||||| | || ||    |||    | ||    |  ||||||||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||
--------------------------------------------------------------------------------------ttttcttaaacatttgc-----ttactgcaagaaaatatgcattgattttcactgataatgtgcctttgttacacaaactggttaactgtatttggcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGACCGTGTGGGACCAAACCGTTGAGTATTGTGCATTCGCTTATCAGCAGTAT

upper sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 13
gtatatatttaagtatgttctttttacattttatgctagttcctgattcctgtagtgtctggatagttatttcttggctgatacattgctctgatgtacctgtaaagttcactttgcttccttgtactatgatctaaacagctaacatctttgtgagactaaaaattacattttaaatt-------ggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGACTGTGTGGGACCAAACTGTTGAGTATTGTGCATTTGCTTATCAGCAGTAT
                                                                                                     || ||  | |   |  ||  |     ||  |    ||   |  |  | ||    ||| |  | || || |||||| ||       | | ||| |||||||| | |||||||||  | ||  ||||| | || || || |||||||  ||||||||||| |||||||| ||||||||||| || ||||| || 
-----------------------------------------------------------------------------------------------------gtgaaacttataat-ttttgtgagggtacaactacaagttcacaagttttctatagatttgacatcactttttaattttgtttgtgattcagTTGGGAGACATTTCAGCCTGTGGGGGGTTTACTTCCTCAGCCAGAATGGACTGCTTGGGACCAAACCGTTGAGTACTGTGCATTTGCATACCAGCAATAC

upper sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0056g00040.t01 (Vitis vinifera), 3'ss of exon 14
gtatatatttaagtatgttctttttacattttatgctagttcctgattcctgtagtgtctggatagttatttcttggctgatacattgctctgatgtacctgtaaagttcactttgcttccttgtactat-gatctaaacagctaacatctttgtgagactaaaaattacattttaaattggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGACTGTGTGGGACCAAACTGTTGAGTATTGTGCATTTGCTTATCAGCAGTAT
                                                                  || || |||   |  |||  |  | || ||| | |  || |   |  | | |    | | || | ||| | |           |||| ||  | |  |||     ||||||     ||||| ||||| || | | |||||||  |||| || ||  | || || || |||||||  ||||||||||||||||| |||||||| |||| ||||||||| || 
------------------------------------------------------------------tttttcctt--tttgtactgtattttggtgtgc-tacaatggatatctcgttagtgtttgctgttgatttca-----------ctttatgttaatgcaaa----gttttaa---tatgcagTTGGGAAACTTTTGAGCCTGTGGGTGGTCTCCTCCCTCAGCCAGAATGGACTGCTTGGGACCAAACTGTTGAATATTGTGCTTTTGGTTATCAGCAATAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|31364251|gb|CD448606.1|CD448606
EST:     GATCCATTTTCCTCTAAGGAAGGGCCTCCACAAAATTTCCAACTGTACAG                         CTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGAC
genomic: GATCCATTTTCCTCTAAGGAAGGGCCTCCACAAAATTTCCAACTGTACAGgtatatattt ... attggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGAC
EST: gi|71428569|gb|DR809619.1|DR809619
EST:     GATCCATTTTCCTCTAAGGAAGGGCCTCCACAAAATTTCCAACTGTACAG                         CTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGAC
genomic: GATCCATTTTCCTCTAAGGAAGGGCCTCCACAAAATTTCCAACTGTACAGgtatatattt ... attggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctaaacagctaacatctttgtgagactaaaaattacattttaaattggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGACTGTGTGGGACCAAACTGTTGAGTATTGTGCATTTGCTTATCAGCAGTAT
                         gactaaa  putative branch site (score: 2)
                        agactaaaaattacat  TA-rich tract