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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accatatttctgcgcattctcagctaaatatgcatggatgtgaacttggatatatctcctgtcatgtcgttgattaccttttctctctctttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTGTATTTCGATGGTTAGGCCTGAGCCAGCCATCCCACTTACCCCTAGCAGA

Basic information

species Zea mays
transcript GRMZM2G071378_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071378_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 2
----------accatatttctgcgcattctcagctaaatatgcatggatgtgaacttggatatatctcctgtcatgtcgttgattaccttttctctctctttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTGTATTTCGATGGTTAGGCCTGAGCCAGCCATCCCACTTACCCCTAGCAGA
          || | |||| || || | |||  || || || ||   |  | |  |     |||     || |||||   ||| |   |||| | |       ||| ||||||| ||||||||||| |||||||||||||| || |||||||||||||| || ||||| ||||||||||| |||||||| |||||||||||  || ||||
gttgtgtccaacaagatttatgggc-tgctc--ctcaacatacacatacttcatttgtatgataatggatgccatgtaactgactgtgttttgtat-------tttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA

upper sequence: GRMZM2G071378_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 3'ss of exon 2
--accatatttctgcgcattctcagctaaatatg-catggatgtgaacttggatatatctcctgtcatgtcgttgattaccttttctctctctttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTGTATTTCGATGGTTAGGCCTGAGCCAGCCATCCCACTTACCCCTAGCAGA
  |||| |||| || || | | |  | | || |  |||   | |||   ||||  ||||||||| |||| | |   | ||   || | |    | |||| ||||||| || |||||||| |||||||||||||| || |||||||||||||| || ||||| ||||||||||| |||||||| ||||||||||| ||  ||||
caaccagatttatgggc-tgcccctcaacatgtttcatttgtatgataatggaattatctcctgccatgccat--gtaactgattatgttctgtgttttgcagCCACAACCTTAACTGGCCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCACTGCCAGA
















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|71309814|gb|DR791189.1|DR791189
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|60394732|gb|DN227602.1|DN227602
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|149076589|gb|EE165223.2|EE165223
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324149|gb|FL195965.1|FL195965
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATCA
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATT-
EST: gi|148931458|gb|EC874447.2|EC874447
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324154|gb|FL195970.1|FL195970
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATCG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324155|gb|FL195971.1|FL195971
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGAC
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGAC
EST: gi|149078292|gb|EE167056.2|EE167056
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324147|gb|FL195963.1|FL195963
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGAC-ACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324153|gb|FL195969.1|FL195969
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|148968976|gb|EE019670.2|EE019670
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324145|gb|FL195961.1|FL195961
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGAC
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGAC
EST: gi|211324144|gb|FL195960.1|FL195960
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATCG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|67041554|gb|CO467809.1|CO467809
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATCG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|76282823|gb|DV022391.1|DV022391
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211324143|gb|FL195959.1|FL195959
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATCG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|211321984|gb|FL195958.1|FL195958
EST:     CTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATCG
genomic: CTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGG-ATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
EST: gi|71446961|gb|DR828011.1|DR828011
EST:     ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTG                         CCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG
genomic: ACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgt ... ttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatatatctcctgtcatgtcgttgattaccttttctctctctttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTGTATTTCGATGGTTAGGCCTGAGCCAGCCATCCCACTTACCCCTAGCAGA
                      cgttgat  putative branch site (score: 5)
                   tgtcgttgattacctt  CT-rich tract
                                          tcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accatatttctgcgcattctcagctaaatatgcatggatgtgaacttggatatatctcctgtcatgtcgttgattaccttttctctctctttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTGTATTTCGATGGTTAGGCCTGAGCCAGCCATCCCACTTACCCCTAGCAGA

- - - - - - -gcattct
- - - - - - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg