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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgttcacatttagtacaaaaaacttatcttcaactcttggaggattaggtttaagatacttgctcaccactaggatgcgtagcatcttcactg...

Basic information

species Zea mays
transcript GRMZM2G135283_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 11
GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgttcacatttagtacaaaaaacttatcttcaactcttggaggattaggtttaagatacttgctcaccact--aggatgcgtagcatcttcactg--
||||||||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||||| |||||||  ||||||| ||||  | | |     || | || | ||     | |  | | | |    |  || | || ||||  |  |||  |    ||||||||   
GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtat--gtgttcaaattt--tgctaggtttttttttttatctacaatatggcttgatctttctttatttcacaacacttaataatgattttgttcttcacttag
















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|148973318|gb|EE024403.2|EE024403
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGTTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTTTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|67042253|gb|CO468508.1|CO468508
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|6194529|gb|AW146633.1|AW146633
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|108953686|gb|EC364842.1|EC364842
EST:     AGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: AGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|71299009|gb|DR785497.1|DR785497
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60354435|gb|DN221408.1|DN221408
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60343439|gb|DN210412.1|DN210412
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|40336482|gb|CK370552.1|CK370552
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|113700941|gb|EE678445.1|EE678445
EST:     CAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|6102053|gb|AW126523.1|AW126523
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|67013913|gb|CO442662.1|CO442662
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|37393418|gb|CF633973.1|CF633973
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|166685188|gb|EG257794.1|EG257794
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGAC
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGAC
EST: gi|60397906|gb|DN230722.1|DN230722
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|14204327|gb|BG838004.1|BG838004
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60351519|gb|DN218492.1|DN218492
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTTAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGAC
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGAC
EST: gi|67024112|gb|CO452861.1|CO452861
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60357206|gb|DN224179.1|DN224179
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60353152|gb|DN220125.1|DN220125
EST:     GTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: GTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60349820|gb|DN216793.1|DN216793
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgttcacatttagtacaaaaaacttatcttcaactcttggaggattaggtttaagatacttgctcaccactaggatgcgtagcatcttcactg

- - - - - - - - - AGAGCT
- - - - - - - - -  GAGCTT
- - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - -  AGCAAG