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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatcaccttccgtgcttccttgttactgctatttactgcatctggttcagctctagggccttttatataaatccctaattacgtatggtgtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACAC

Basic information

species Zea mays
transcript GRMZM2G113619_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 8
gcatcaccttccgtgcttccttgttactgctatttactgcatc-tggttcagctctagggccttttatat--aaatccctaattacgtatggtgtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACAC
  | || | |  ||  |   |  |   || ||  | ||| ||  | ||| |      |||  | || | |  || |   |  ||   | |  ||| ||| |||||||| |||||  |||| ||| | |||||||||||||| || ||||| || |||||||  ||||||||||||||||| |||||||| || ||| ||||||
-gagcatcattagt-ttcaataatatttgttagcttctggattgtagttaattcacggggtatcttgttttcaagtgtttgtttcaatgta-tgtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGGCAAGGAACCGGAGTGCATTTCACCATTGCACCGGATTCGCCGACCACAC
















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|76280759|gb|DV020327.1|DV020327
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|37399815|gb|CF637245.1|CF637245
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|78086641|gb|DV515034.1|DV515034
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|19769762|gb|BQ034483.1|BQ034483
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|71766652|gb|DR964589.1|DR964589
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|6827480|gb|AW331123.1|AW331123
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|50325342|gb|CO520468.1|CO520468
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTTTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|78106313|gb|DV524731.1|DV524731
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|93283252|gb|EB675516.1|EB675516
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-                         GA--CAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|19769358|gb|BQ034079.1|BQ034079
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|71311804|gb|DR792363.1|DR792363
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|60338944|gb|DN205917.1|DN205917
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|91877838|gb|EB407795.1|EB407795
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|211143061|gb|FL281156.1|FL281156
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|60337669|gb|DN204642.1|DN204642
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|19822097|gb|BQ048121.1|BQ048121
EST:     ACATCATGGCGTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|78106314|gb|DV524732.1|DV524732
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagctctagggccttttatataaatccctaattacgtatggtgtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACAC
                            ccctaat  putative branch site (score: 3)
                                              tctgtcc  putative PPT
                ttttatataaatccct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatcaccttccgtgcttccttgttactgctatttactgcatctggttcagctctagggccttttatataaatccctaattacgtatggtgtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA