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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggttcttaatatacccatcatctaatattggagttaataaacatgaagtttgtattatgtctgctgtaccatcaccattttgtaatagtttatttagtttgcttgaaattctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG

Basic information

species Zea mays
transcript GRMZM2G138505_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 2
gtgtggttcttaatatacccatcatctaatattggagttaataaacatgaagtttgtattatgtctgctgtaccatcaccattttgtaatagtttatttagtttgcttgaaattctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG
||||||  |   ||||||||||||| |  |  |     |||| |  ||| |||||||| ||||| |   |   ||||| ||| | ||  | ||  | ||  |||||||||| |||| ||  ||||||||||| |  |||||||| || |||||||||||||| ||||||| ||||||||||||||| ||| | |||||||| || || ||||| |||||||||
gtgtggcgca-gatatacccatcatgtgcttctttctgtaatgaggatggagtttgtactatgtata--gatgcatcaacatctagt--ttgtaaaatttatttgcttgaacttctgtgtgcagGGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCTGTACATTCTAGTTCTTTGTTTGTTGGCCGAGAGATTCATAGTGAAAAG
















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|213187878|gb|FM187980.1|FM187980
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATANCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|60401512|gb|DN234319.1|DN234319
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|60398184|gb|DN231000.1|DN231000
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|88751194|gb|DY535335.1|DY535335
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|149081143|gb|EE170252.2|EE170252
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|101387923|gb|EB815975.1|EB815975
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|78081340|gb|DV509752.1|DV509752
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|71772237|gb|DR970174.1|DR970174
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|31355242|gb|CD439599.1|CD439599
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
EST: gi|71447439|gb|DR828489.1|DR828489
EST:     TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAG                         GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT
genomic: TGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCT

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), 42 (downstream exon)
Score: 72

TTCAATGCCTATGGCTATGTCAAAGAACCCAAAGATTGCCTTTATGTTCTTGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG


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

TTCAATGCCTATGGCTATGTCAAAGAACCCAAAGATTGCCTTTATGTTCTTGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

TTCAATGCCTATGGCTATGTCAAAGAACCCAAAGATTGCCTTTATGTTCTTGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 58

TTCAATGCCTATGGCTATGTCAAAGAACCCAAAGATTGCCTTTATGTTCTTGACACCGGGTTCATTGCCTTTTGAGAAGTTGTGGGAGAAATTTTTACAGgtgtggttct ... ctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccatcaccattttgtaatagtttatttagtttgcttgaaattctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG
                                           ttctttgc  CT-rich tract
           attttgtaatagttta  TA-rich tract