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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggacataatgccctttttattctgtaattgttctatttagtaaaaaaaattcatctaactgtttgccatcacctctcatttcttcatggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGATACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTAT

Basic information

species Zea mays
transcript GRMZM2G113619_T04
intron # 6
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 6
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 5
gtaggacataatgccctttt-tattctgtaatt--gttctatttagtaaaaaaaattcatctaact----gtttgcca------tcacctctcatttcttc-atggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGATACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTAT
||||| ||| ||||  || | ||||    |  |  |||||  ||  ||  | |   |  | | | |    || | |||      |  |  |  |||||||      | |  |||||||| ||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||||||||||| |||||||| 
gtagggcatcatgcttttctatattgaagacatgggttcttgttgatattatatcgtggtgtcatttgtagtattccaggctaattgcaacctatttcttttggaatgcacagTGGTGGCTGGACCATTACTGGTACTGCATTTGACTTGCGTGATCCTAGGATCCTTGCAGTTGCACAGAACCACATTATGGAAGCTGAATACGATGATTAC
















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|78086641|gb|DV515034.1|DV515034
EST:     CCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: CCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|78086642|gb|DV515035.1|DV515035
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|78089708|gb|DV518082.1|DV518082
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAAATACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|76280760|gb|DV020328.1|DV020328
EST:     TACACTGCACCTCCCAGAGGGCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGGACA-TTACCGGTACCGCATTTGACTTGCGTGATCCTAGGA
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGG-ACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGA
EST: gi|91053257|gb|EB163675.1|EB163675
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTTGGGTGGACAATTACGGGTACCGC
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGT-GGGTGGACAATTACCGGTACCGC
EST: gi|71424785|gb|DR806435.1|DR806435
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|71766652|gb|DR964589.1|DR964589
EST:     ACACTGC-CCTCCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGGGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: ACACTGCACCT-CCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|166620083|gb|EG102933.1|EG102933
EST:     ATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: ATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|211143062|gb|FL281157.1|FL281157
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     CCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACGGCATTTGACTTGCGTGATCCTAGGAT
genomic: CCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|8551597|gb|BE128942.1|BE128942
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCG
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCG
EST: gi|71766653|gb|DR964590.1|DR964590
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATTCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
EST: gi|440689|gb|T14710.1|T14710
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTNACTTGCGTGATCCTAGG
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGG
EST: gi|76291932|gb|DV031500.1|DV031500
EST:     TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAG                         TGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT
genomic: TACACTGCACCTCCCAGAGGCCATCCTGATGAAACTACCATTGATATAAGgtaggacata ... tggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaattcatctaactgtttgccatcacctctcatttcttcatggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGATACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTAT
           atctaac  putative branch site (score: 2)
                              cctctcatttcttcat  putative PPT
     aaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggacataatgccctttttattctgtaattgttctatttagtaaaaaaaattcatctaactgtttgccatcacctctcatttcttcatggttcctagTGGTGGGTGGACAATTACCGGTACCGCATTTGACTTGCGTGATCCTAGGATACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA