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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctacgttgccgatttctcttcatgttgcgcaaacaattttggttttgatgctaccatcatatatgcactagacttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG

Basic information

species Zea mays
transcript GRMZM2G162672_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 9
gtatgatctacgttgccgatttctcttcatgttgcgcaaacaattttggttttg-atgctacca-tcatatatgcactagacttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG
|||  ||  ||  ||| ||| |   | ||| ||| | ||| |  | || | ||  |||| |  | | | || |  |    |  |  | |   | || || ||||||||||||||||||| ||||||||||| ||||| || |||||  ||||| ||||| ||||||| ||||||||||||
gta-aattaacagtgcggatcttcttccatattgagtaaaaatctatgatattatatgcaagaaattagatgtatatcctatctgtatg---tattcttcgcagGTGGGCTGGCCAGGCATTATTTGGAACCCTTACTCCTGATATTGTTGTCCTGACTTCTTTGTATAGCATAGCTGGG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 9
gtatgatctacgttgccgatttctcttca-tgttgcgcaaacaattttggttttgatgctaccatcatatatgcactagacttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG
   ||||  |  |   |  ||| | || | |  |  |     | || |  |||     ||  ||   ||| |        ||| |  ||||| ||  |  ||||||||| || ||||| || ||||||||||||||||||||||| |||||  | ||     | |||||||||||||| 
---tgattaaactgatccttttttatttactaataagtgttaagttctattttctggacttgcactgtatctcagaagatcttgattggtttcttactgacagGTGGGCAGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGA

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 9
gtatgatcta-cgttgccgatttctcttcatgttgcgcaaacaattttggttttgatgctaccatcatatatgcactaga-cttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG
 ||   |  | |      || || | | | |  |  | |   | || |  |||     ||  ||   ||| | ||  ||| ||| |  ||||| ||  |  |||||||||||| ||||| || ||||||||||||||||||||||| |||||  | ||     | |||||||||||||| 
-tacatttcatcaacatagaattatttac-taataagtattaagttctattttctggacttgcactgtatct-cataagatcttgattggtttcttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG-

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 1
gtatgatctacgttgccgatttctcttca-tgttgcgcaaacaattttggttttgatgctaccatcatatatgcactagacttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG
   ||||  |  | | |  ||| | || | |  |  |     | || |  | |     ||  ||   ||| |        ||| |  ||||| ||  |  ||||||||| || ||||| || ||||||||||||||||||||||| |||||  | ||     | |||||||||||||| 
---tgattaaactggtccttttttatttactaataagtgttaagttctattatctggacttgcactgtatctcagaagatcttgattggtttcttactgacagGTGGGCGGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGA

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|149038823|gb|EE155536.2|EE155536
EST:     GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
EST: gi|211036106|gb|FL230098.1|FL230098
EST:     GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
EST: gi|61119511|gb|DN560472.1|DN560472
EST:     GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
EST: gi|211036107|gb|FL230099.1|FL230099
EST:     GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
EST: gi|78120047|gb|DV538431.1|DV538431
EST:     GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
EST: gi|71426127|gb|DR807177.1|DR807177
EST:     GGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
EST: gi|149080582|gb|EE169625.2|EE169625
EST:     GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTG                         GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT
genomic: GGATGGATTGGGAACTTCGCTCTGGGTGCGAGTTACATCAGCTTGCCCTGgtatgatcta ... ttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttgatgctaccatcatatatgcactagacttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG
  ttttgat  putative branch site (score: 4)
                                         ttttttttttgc  putative PPT
                                         tttttttttt  TA-rich tract