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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggccctctttttgacgtagtcttcttgttgccattctttcttggagtatatgttgacatggtgttgtgacatttgcccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA

Basic information

species Zea mays
transcript GRMZM2G037698_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037698_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 15
gtatggccctctttt-tgacgta-------gtcttcttgttgccattctttcttggagtatatgttgacatggtgt-tgtgacatttgcccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA
||  | |||| | || || |  |       |  |  |  ||| |||   | |||| | |  |   | |  |||| | |||| | |   |  |||  |||||||||| ||    || ||||| ||  | ||||| |||||||| ||||||||||||||||| || || |||||||||||||| |  || ||||| ||  |
gttcgtccctttcttatggcccacattctcggttcgtgattggcatctgtgcttgcacttaac--taatttggtttctgtggcgtacacttttct-cagGGAAAGTGACAAACGTCAAGTTTGGCACCGATGCGAAGTACATTGCCGTAGGTTCTATGGATCGTAACCTACGGATATTTGGGCATCCGGGAGAAGATGA
















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|211149654|gb|FL454000.1|FL454000
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|32908360|gb|CF013173.1|CF013173
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAG
EST: gi|5055844|gb|AI734731.1|AI734731
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGG
EST: gi|32934237|gb|CF039049.1|CF039049
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
EST: gi|78544020|gb|DV621518.1|DV621518
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|33090853|gb|CF050847.1|CF050847
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
EST: gi|32933281|gb|CF038093.1|CF038093
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
EST: gi|5713843|gb|AI943828.1|AI943828
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|32936163|gb|CF040975.1|CF040975
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|32837457|gb|CD977135.1|CD977135
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
EST: gi|148940044|gb|EC884787.2|EC884787
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|21391194|gb|BQ529243.1|BQ529243
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|166410938|gb|EG060200.1|EG060200
EST:     CATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: CATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|78543890|gb|DV621388.1|DV621388
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|20336919|gb|BQ172549.1|BQ172549
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|33103734|gb|CF063694.1|CF063694
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
EST: gi|211124458|gb|FL005597.1|FL005597
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTG-AACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctttcttggagtatatgttgacatggtgttgtgacatttgcccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA
                   tgttgac  putative branch site (score: 3)
                                        tttgcccttcc  putative PPT
               tatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggccctctttttgacgtagtcttcttgttgccattctttcttggagtatatgttgacatggtgttgtgacatttgcccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA