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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctcaaatgaacacacatattatctgtgtggtatttcgaggtagtatatacataggttgactaatctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG

Basic information

species Zea mays
transcript GRMZM2G420865_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 3
gtatctcaaatgaacacacatattatctgtgtggtatttcgaggtagtatatacat--aggttgactaatctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
|||| |  ||| |||| | |  |    |  |  | |||| ||   ||||| ||  |  || || | | | |||||||   ||||||||||||||||| || |||||| |||||||||||||||| || || || |||||||||||||||||||||||||| ||||||||||| ||||||||||
gtatatataattaacaaaaacttccctttgggagcattttgaatcagtatctatctttagcttaattgaactcttta---tagACAGCTGCTTTCTCATTACCTGTGCTGGAACGTCTACTTTTCCGGCCCAAACGTGTACCTGCAATTAGGGTGCTTATCCTTACTCCAACAAGAGAGTTGG

upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G25240.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------gtatctcaaatgaacacacatattatctgtgtggtatttcgaggtagtatatacataggttgactaatctctttaagt-tagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
                                                          || |      |||       ||| ||  ||||  | |||  |     | | | ||||   || ||| | | |||   |  |||||||||| ||  |  | |||   || ||  |  |  | || |||||||||||  | | |||||| ||||| || ||||||||||| |||||||||||||
gtaatctctttgttactttctttgggtgtttgttaatttgtgatgccttgcttctgtggtttggtgcctgagtttctgtatgatg-gtgtt-tcttttaatcccctttgttcatatcctg-ctattgtgtttccatgcagACAGCTGCATTTGCACTACCTACTTTAGAGAGGTTGTTGTTCCGTCCAAAGCGCATGCGTGCAATAAGGGTCCTCATTCTTACTCCGACCAGAGAGTTGG

upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 3
-------------gtatctca-aatgaaca-----cacatattatctgtgtggta-tttcgaggtagtatatacataggttgactaatctctttaagt-tagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
             || |||   ||||  |      || || ||     |||| |  |||  | |   | | | ||||  ||| ||| | | |||   |  |||||||||| ||  |  | |||   || ||  |  |  | || |||||||||||  | | |||||| ||||| || |||||||||||||||||||||||| 
atcttgctattgtgtttcttttaatgccctttgttcatatcttgctattgtgtttcttttaatgccctttgttcatatcttg-ctattgtgtttccatgcaGACAGCTGCATTTGCACTACCTACTTTAGAGAGGTTGTTGTTCCGTCCAAAGCGCATGCGTGCAATAAGGGTCCTCATTCTTACTCCAACCAGAGAGTTG-

upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------gtatctcaaatgaacacacatattatctg-----tgtggtatttcgaggtagtatatacata--ggttgactaat-ctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
                                                                  | |  | ||||  ||  |  |  | |||     |    || ||   |||  | |  | |||  | ||    | | ||| || |   |||| ||||| || || || |||   || ||  |  || | || |||||||| ||||| |  ||||| ||||| ||| ||||||||||||||||||||||||
gtatgttgtgcgtcttgggtgcttgtgtaattgactctataatgtactactatgaaaacgagttgattttactaatgggcaagctgaaaaactgaaaccttctctagttatcggttctgtgaaaataatgatttgggattgctcctttacacagACGGCTGCCTTTTCCTTACCTACATTAGAGAGGTTATTGTTCCGTCCAAAACGTGTGCAAGCAATCAGGGTCCTTGTTCTTACTCCAACCAGAGAGTTGG

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|67017959|gb|CO446708.1|CO446708
EST:     CATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAG                         ACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAG
genomic: CATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAGgtatctcaaa ... tttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgtggtatttcgaggtagtatatacataggttgactaatctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
                                   gactaat  putative branch site (score: 2)
                                         tctcttt  CT-rich tract
                     tatatacata  TA-rich tract