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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaccactggtggttcattgcctcatttttatatgctaaagcaataaaaccactaatggttcattccctgacattatgtccctcatttgtacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG

Basic information

species Zea mays
transcript GRMZM2G497531_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G497531_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
---gaaccactggtggttcattgcctcatttttatatgctaaagcaataaaaccactaatggttca-ttccctgacattatgtccctcatttgtacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG
    |||      | | | ||| | | |  ||  || |    | | |||    ||     |||| | |||  | |  ||   |     | |||||||| | |||| ||||| || ||| |||||||||| || |||||| |||||||  |||| || ||||||||| ||||||||  || ||  |||||||||||
accaaactggaactaggttattacgttacattattacg----aactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
















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|113701349|gb|EE678853.1|EE678853
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|71770222|gb|DR968159.1|DR968159
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|149080545|gb|EE169584.2|EE169584
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTTTATTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|76919725|gb|DV167838.1|DV167838
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|76919723|gb|DV167837.1|DV167837
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTTTATTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|40303072|gb|CK347459.1|CK347459
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|149080546|gb|EE169585.2|EE169585
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|16925963|gb|BM079031.1|BM079031
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|149078398|gb|EE167172.2|EE167172
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
EST: gi|211277613|gb|FL433176.1|FL433176
EST:     TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC
genomic: TCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGAC

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: 117

CAATCCCGACACAGTATGTCCTCAATCAGCACTGCTGCACAACCTAATGATCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

CAATCCCGACACAGTATGTCCTCAATCAGCACTGCTGCACAACCTAATGATCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

CAATCCCGACACAGTATGTCCTCAATCAGCACTGCTGCACAACCTAATGATCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CAATCCCGACACAGTATGTCCTCAATCAGCACTGCTGCACAACCTAATGATCAGCATGCTTCTGGAAGTAGCAGCTCCCCAAATGAATTTGTAAATCAAGgtaaattagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaccactaatggttcattccctgacattatgtccctcatttgtacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG
                         acattat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaccactggtggttcattgcctcatttttatatgctaaagcaataaaaccactaatggttcattccctgacattatgtccctcatttgtacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - ctggtgg
- - - - - - - - - - - - - - - - atgctaa
- - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatttg