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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttttattaatgcattgcaattacatcagatgtattgaagattatgtttacataaatattatgttggccctttttcttacttcattaaatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT

Basic information

species Zea mays
transcript GRMZM2G020728_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2
-tgcttttattaatgcattgcaattacatcagatgtattgaagattatgtttacataaatattatgt----tggccctttttcttacttcat----taaatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
  |  |  ||||     ||  |||  | | || |  || |||||   ||      ||||| || ||     ||   |||   | ||||  ||    | |  ||| |   |  |    | |     |  | |||||||||| | ||||||||| |||||||||||||||||||| ||||||| ||||||||||||||||||         
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA---------

upper sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 1
-tgcttttattaatgcattgcaattacatcagatgtattgaagattatgtttacataaatat----tatgttggccctttttcttacttcat----taaatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
  |  | |||||     ||  |||  | | || |  || |||||   ||       |||| |     ||  ||   |||   | ||||  ||    | |  ||| |   |  |    | |  |  |  | |||||||| | | ||||||||| |||||||||||||||||||| ||||||| ||||||||||||||||||         
tagtgtgtattatgttcttataatctcttgagttcgatggaagagcttgaccgtgcaaatgtattgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCGCTCGACGTTCATTGACAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA---------
















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|9825051|gb|BE575253.1|BE575253
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|78123212|gb|DV541596.1|DV541596
EST:     GGTGCAGATTGGAGATCCGCCCGGATTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCTTTGGAGTGCTCCTTTCTTTGAGACAGCATGCCTAAAATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211306393|gb|FL121401.1|FL121401
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211436976|gb|FL408938.1|FL408938
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|22546324|gb|BU098635.1|BU098635
EST:     GG-GCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211481609|gb|FL376536.1|FL376536
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211121008|gb|FL425228.1|FL425228
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATARAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211254317|gb|FL400890.1|FL400890
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|89251444|gb|DY623230.1|DY623230
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|22472255|gb|BU036735.1|BU036735
EST:     GG-GCAGA-TGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211022015|gb|FL261314.1|FL261314
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|26456977|gb|CA828560.1|CA828560
EST:     GG-GCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211484707|gb|FL383650.1|FL383650
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|37396850|gb|CF635719.1|CF635719
EST:     GATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211262096|gb|FL418805.1|FL418805
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|26457042|gb|CA828625.1|CA828625
EST:     GG-GCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|20811232|gb|BQ295710.1|BQ295710
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|211476224|gb|FL261311.1|FL261311
EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATT-AGGCAGCATGCCTAA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAA
EST: gi|60349541|gb|DN216514.1|DN216514
EST:     GCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|9794575|gb|BE552883.1|BE552883
EST:     GGTGCAGA-TGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA
EST: gi|22543112|gb|BU093550.1|BU093550
EST:     NG-GCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: -GTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttacataaatattatgttggccctttttcttacttcattaaatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
                              ttcttac  putative branch site (score: 2)
                                              tgttccc  putative PPT
     tacataaatattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttttattaatgcattgcaattacatcagatgtattgaagattatgtttacataaatattatgttggccctttttcttacttcattaaatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
tgctttt
- - - - - -atgcatt
- - - - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgttg