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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccggagaaatacttgtggttcatcacatcatttttatattataataaagcaagatgcttcattcactggtactctgtcccttcatttgcacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGCTTAATTCTCAGGGTCAACAAAGTCAAGAACCAAAAATAAG

Basic information

species Zea mays
transcript GRMZM2G180967_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180967_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
tccggagaaatacttg--tggttcatcacatcatttttatattataataaagcaagatgcttcattcactggtactctgtcccttcatttgcacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGCTTAATTCTCAGGGTCAACAAAGTCAAGAACCAAAAATAAG
 ||  |     ||| |  |  | | | |||| |||   | | ||||   |      | | |   |||  |  |  |   |   |  | ||| |||| | |||| ||||| || ||| |||||||||| || |||||| |||||||| ||||||  ||||||||| ||||||||  || ||| |||||||||||
accaaactggaactaggttattacgttacattattacga-actatacgtacatgttaggttaagttcttttatgttg-attattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
















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|18177051|gb|BM378261.1|BM378261
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|37390208|gb|CF632332.1|CF632332
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|60350874|gb|DN217847.1|DN217847
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|67019343|gb|CO448092.1|CO448092
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|37373776|gb|CF623206.1|CF623206
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|18177085|gb|BM378295.1|BM378295
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|101392744|gb|EB818303.1|EB818303
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|44901241|gb|CK827786.1|CK827786
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|37384603|gb|CF629391.1|CF629391
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|211155651|gb|FL446893.1|FL446893
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|18176953|gb|BM378163.1|BM378163
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|40336079|gb|CK370149.1|CK370149
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|18179467|gb|BM380677.1|BM380677
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|71317315|gb|DR795345.1|DR795345
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|40303076|gb|CK347463.1|CK347463
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|211243388|gb|FL072668.1|FL072668
EST:     TCAGCATGTCTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|91876027|gb|EB405984.1|EB405984
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|211243389|gb|FL072669.1|FL072669
EST:     CAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTTGTAA-TCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: CAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTT-GTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|14245512|gb|BG874094.1|BG874094
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
EST: gi|13249771|gb|BG360676.1|BG360676
EST:     TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAG                         GTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC
genomic: TCAGCATGTTTCTGGAACTAGCAGCTCCCCAAATGAGTTTGTAAATCAAGgtaaactagt ... acaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagcaagatgcttcattcactggtactctgtcccttcatttgcacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGCTTAATTCTCAGGGTCAACAAAGTCAAGAACCAAAAATAAG
                                    ttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccggagaaatacttgtggttcatcacatcatttttatattataataaagcaagatgcttcattcactggtactctgtcccttcatttgcacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGCTTAATTCTCAGGGTCAACAAAGTCAAGAACCAAAAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - gagaaata
- - - - - - - - - gttcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcac