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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccttgccctttcttctttgggacaattgtgattatacccttcgctggtcttgcaattgtgattttaccctccgttttccaactttgtgttcatagataagctattctggacaattcaatgttatagattagataggctcacaagcatttagctctgtggttgtgatgaaattgcacttataacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT

Basic information

species Zea mays
transcript GRMZM2G163233_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163233_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 6
gtatgccttgccctttcttctttgggacaattgtgattatacccttcgctggtcttgcaattgtgattttaccctccgttttccaactttgtgttcatagataagctattctggacaattcaatgttatagattagataggctcacaagcatttagctctgtggttgtgatgaaattgcacttataacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT
                                                                                       ||       ||  | |  ||| | |         ||| || |  | ||| | | ||||  | |||  |  | | | |   | |     |     ||  |  || |||||||||||| || || ||||||||||| ||||||||    ||||| || |||||||| || |||||||| ||||||||||||||||| |||||||| || |
---------------------------------------------------------------------------------------ttcaaacaaatgaaaaccctaatttatctg---taatttttttaagtag-tggactca--aacat--aaatattttgaaataacaccgtcaactttcaatttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT
















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|12046041|gb|BF728180.1|BF728180
EST:     CAAGTTTCTGGTGTGAGAGCATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|211415631|gb|FL375675.1|FL375675
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|5296291|gb|AI783061.1|AI783061
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|409609|gb|T12671.1|T12671
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAAAATGATTTCCAG                         ATTCTGCGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|211345775|gb|FL379635.1|FL379635
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|6760563|gb|AW324662.1|AW324662
EST:     CAAGTTTCTGGTGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|60398362|gb|DN231178.1|DN231178
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|40334122|gb|CK368192.1|CK368192
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|15590209|gb|BI674825.1|BI674825
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|211154199|gb|FL451794.1|FL451794
EST:     CAATTTTGAAGAGAATGATTTCCAG                         ATTYTACGAGTTCTCATGACAATCATTGACACATCAAGTGACMCCMCCGCT
genomic: CAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|60353239|gb|DN220212.1|DN220212
EST:     CAAGTTTCTGGTGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTTTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|78026061|gb|DV494448.1|DV494448
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|32915729|gb|CF020541.1|CF020541
EST:     GCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: GCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|71757598|gb|DR955535.1|DR955535
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
EST: gi|37373833|gb|CF623239.1|CF623239
EST:     CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAG                         ATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT
genomic: CAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 114

ACAGCAAGTTCTTCTTGGTCATCTTGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

ACAGCAAGTTCTTCTTGGTCATCTTGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

ACAGCAAGTTCTTCTTGGTCATCTTGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 194

ACAGCAAGTTCTTCTTGGTCATCTTGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttg ... aacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcacaagcatttagctctgtggttgtgatgaaattgcacttataacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT
                                         ttataac  putative branch site (score: 194)
                                         ttataactt  TA-rich tract