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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagctaagactggtattgtttggcatgtcataatatattagttgtctcaactcttcaaatttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGAGGGTGTGGCAGAACGGGTATCTCGTAGAAGCCATGAAATTCTGGGCC

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 11
gtgcagctaagactgg--tattgtttggcatgtcataatatattagttgtctcaac-tcttcaaatttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGAGGGTGTGGCAGAACGGGTATCTCGTAGAAGCCATGAAATTCTGGGCC
||   | |||||||     ||||||||  |     || ||| ||| |   |||||| | ||| ||||    |  ||||||| ||||||||||| || ||||||||||| ||||||||||| |||||||||||||||||||| |||||| |||| ||||| ||||||||||| || |
gtaaggttaagactttctcattgtttgtaac--tgtactatgttaat---ctcaaccttttctaattgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGAC
















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|31664298|gb|CD573023.1|CD573023
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCNCCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60400512|gb|DN233319.1|DN233319
EST:     TACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: TACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|4837587|gb|AI670677.1|AI670677
EST:     GCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|31405984|gb|CD484716.1|CD484716
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60356069|gb|DN223042.1|DN223042
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60357001|gb|DN223974.1|DN223974
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|32847446|gb|CD987127.1|CD987127
EST:     GATATTACTTTGTCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCGCCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|110218916|gb|EC900814.1|EC900814
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|110532935|gb|EE037115.1|EE037115
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|32912299|gb|CF017111.1|CF017111
EST:     ATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: ATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|149096473|gb|EE182215.2|EE182215
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|211425320|gb|FL461581.1|FL461581
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|37375908|gb|CF624436.1|CF624436
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGT-ACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|71304924|gb|DR788592.1|DR788592
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|33103241|gb|CF063201.1|CF063201
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60338462|gb|DN205435.1|DN205435
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|211096440|gb|FL454801.1|FL454801
EST:     GCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|32938473|gb|CF043292.1|CF043292
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|33098312|gb|CF058272.1|CF058272
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|8666086|gb|BE186902.1|BE186902
EST:     GATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60343320|gb|DN210293.1|DN210293
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|32911368|gb|CF016180.1|CF016180
EST:     ATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: ATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttggcatgtcataatatattagttgtctcaactcttcaaatttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGAGGGTGTGGCAGAACGGGTATCTCGTAGAAGCCATGAAATTCTGGGCC
                                            tttccat  CT-rich tract
         atgtcataatatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagctaagactggtattgtttggcatgtcataatatattagttgtctcaactcttcaaatttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGAGGGTGTGGCAGAACGGGTATCTCGTAGAAGCCATGAAATTCTGGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC