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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagttcaattcacatactgttacaatgaactgtgcttcttttgttgaaatcctgagtattgatgcatttgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT

Basic information

species Zea mays
transcript GRMZM2G466281_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g02750.3 (Oryza sativa), 3'ss of exon 2
gtaagagttcaattcacatactgttacaatgaact---gtgcttcttttgttgaaatcctga----gtattgatgc-att--tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
|| ||||| |    ||||| ||| ||| |||||||   ||  |  ||||||| ||   ||||    | |||| | | |||  |||||||||||||||||||||||| |||||||||||| ||||||| |||||||||||||||
gtgagagtcccg--cacatgctgatactatgaactagggttttctttttgttcaagagctgacaaagcattgtttccattcctgttttccagATTACACTGACAGGCTTCATGTTTCTATTGACATCGGCATTCCTTGGCTTT
















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|211250318|gb|FL201841.1|FL201841
EST:     CCGCTATGGTTTSCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCGCTATGGTTC-CCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|101388019|gb|EB816024.1|EB816024
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|76933447|gb|DV173462.1|DV173462
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|78108358|gb|DV526776.1|DV526776
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|76284393|gb|DV023961.1|DV023961
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|211250321|gb|FL201844.1|FL201844
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|211250315|gb|FL201838.1|FL201838
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATTCAGCATTCCTTGGCTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACAT-CAGCATTCCTTGGCTT
EST: gi|148930548|gb|EE285169.2|EE285169
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|148948015|gb|EC893516.2|EC893516
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|149095953|gb|EE181619.2|EE181619
EST:     CCCGCTACGCTTCCCACCGAACATG                         ATTACAATGAC
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGAC
EST: gi|211250319|gb|FL201842.1|FL201842
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|149085392|gb|EE174899.2|EE174899
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|88756189|gb|DY540330.1|DY540330
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|211250320|gb|FL201843.1|FL201843
EST:     CCCGCTATGGTTTCCACNNAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCC
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCC
EST: gi|88756155|gb|DY540296.1|DY540296
EST:     CCCGCTATGGTTCCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
EST: gi|211250316|gb|FL201839.1|FL201839
EST:     CCCGCTATGGTKNCCACCGAACATG                         ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
genomic: CCCGCTATGGTTCCCACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 148

ACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 126

ACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 117

ACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 232

ACCGAACATGgtaagagttc ... tgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaactgtgcttcttttgttgaaatcctgagtattgatgcatttgttttccagATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT
                                 tattgat  putative branch site (score: 232)
                                           tttgttttcc  putative PPT
                                          atttgtttt  TA-rich tract