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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaggctttccagtttgtttcttgcttctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT

Basic information

species Zea mays
transcript GRMZM2G003509_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
----------------gtatgaggctttccagtttgtttcttgcttctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT
                  || |  ||| |   |  |    |||| |   |    |    ||| |  |    |  ||  | || || |||   | || | |||| | ||||||||  | |||||| ||||  |  |||| | ||||||||||||||| |||||||| || |||||||||||||| ||||||||  |  ||||||
atcccgattcttctccacataatccttgctcat--gacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctat-gcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT

upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
--------------------gtatgaggctttccagtttgttt--cttgctt---ctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT
                    || |   | ||    ||||  ||  |||  |    | || |  |     |    |  |  || | ||  |   |    || || | | |||| ||||||| || || |||||  ||||    || || |||||||||||||| || || |||||||||||||| ||||| || ||||| |  || || || |
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgaggctttccagtttgtttcttgcttctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttg--cagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT
|| ||     | | |       ||  |  |     |  |||  ||  | |    ||||      ||     || | |||| |||  ||| | || |||||| | |||||  ||| |   || | |||||| ||||||||||| || || ||||||||||| |||||||| |||||||| ||||| || |
gtttgctttatactaaagacactcagggattcttaaagatgagttattgaa---attgaattcttggtttcttttttgcttttgtccagCTTTGTAGCGGCGTTGATGAAAATGTGGTTGGAGGTTGTGCTCAGCTTGTCTTTGCCCCAATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatgaggctttccagtttgtttcttgcttctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgc--agTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT
   |  | |||   | |||   ||     | |      ||| |  | |   | | |  ||||  |  |  ||| |    |||||   || | || |||||  | |||||  ||| |   || | ||||||||||||||| || || |||||||||||||| |||||||| |||||||| ||||| || |
--gtttgacttcatactttaactccaaagttt----ctatgctcctttgttctcttcatgacattttgg-attcttgattcttgtctagCTTTGTAGCGGTGTTGATGAAAATGTGGTTGGAGGTTGTGCACAGCTTGTATTTGCCCCTATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

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|211416749|gb|FL321414.1|FL321414
EST:     CTTTAGC-ATGANCGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAA                         TTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC
genomic: CTTTAGCCATGA-CGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAGgtatgaggct ... gctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC
EST: gi|211510674|gb|FL361528.1|FL361528
EST:     GCTTTAGCCATGACGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAA                         TTGTGCAGCGGCATCGATGARGATGCGCCGGGTGCTTGTGCACAGCTTGTC
genomic: GCTTTAGCCATGACGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAGgtatgaggct ... gctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC
EST: gi|211126699|gb|FL314385.1|FL314385
EST:     GCTTTAGCCATGACGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAA                         TTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC
genomic: GCTTTAGCCATGACGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAGgtatgaggct ... gctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC
EST: gi|61119215|gb|DN560176.1|DN560176
EST:     GCTTTAGCCATGACGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAG                         TTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC
genomic: GCTTTAGCCATGACGAGGTTCTTATGTCCCCGGATATGTTTCTTCTGCAGgtatgaggct ... gctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT
            ttctcac  putative branch site (score: 2)
                                          tctgctctt  putative PPT
                                    acattat  TA-rich tract