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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acactttatcagagaaaatcaaagaaaaaaagaactatgacagtacttgaatgataagaatttcaaaagatttatcttacttttttctcatgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGATGTAGAAATTGATGGCCAACACATAG

Basic information

species Zea mays
transcript GRMZM2G158237_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158237_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 1
acactttatcagagaaaatcaaagaaaaaaagaactatgacagt-acttgaatgataagaatttca----aaagatttatcttacttttttctcatgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGATGTAGAAATTGATGGCCAACACATAG
      | |  |||| |      |         |   ||  ||| ||| |   ||  |  |||  |    | ||| |  |  | ||| |||||||  ||| | || || ||| |||||||| |||||| ||||||||| ||||||| ||| | ||||| ||||||||||| ||||| ||||
-----atctgggagataggttctggcctcggttatggtggtagtgactagtgagacgatgattcaatgttacagaatatttattcttctttctcaccttgtacagAGCCTTGGAGAGGTTCGATTACCTGCAGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG
















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|211434807|gb|FL427281.1|FL427281
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211431653|gb|FL404571.1|FL404571
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211093050|gb|FL420421.1|FL420421
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211109670|gb|FL337450.1|FL337450
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|30704819|gb|CD058611.1|CD058611
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211300966|gb|FL391501.1|FL391501
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211229694|gb|FL389659.1|FL389659
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211256545|gb|FL390498.1|FL390498
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|67015837|gb|CO444586.1|CO444586
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211521053|gb|FL387965.1|FL387965
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211182577|gb|FL404772.1|FL404772
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211534860|gb|FL340389.1|FL340389
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211057736|gb|FL416996.1|FL416996
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|88755062|gb|DY539203.1|DY539203
EST:     TCGCGTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCATTTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211402954|gb|FL382690.1|FL382690
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211194087|gb|FL377670.1|FL377670
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211373857|gb|FL385822.1|FL385822
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211211751|gb|FL376364.1|FL376364
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|78080821|gb|DV509233.1|DV509233
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211061094|gb|FL320234.1|FL320234
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211341298|gb|FL394244.1|FL394244
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCARAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|26558040|gb|CA830275.1|CA830275
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|76922696|gb|DV169126.1|DV169126
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|91877249|gb|EB407206.1|EB407206
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|31355561|gb|CD439918.1|CD439918
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211076170|gb|FL369895.1|FL369895
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|21843567|gb|BQ704148.1|BQ704148
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
EST: gi|211163731|gb|FL337956.1|FL337956
EST:     TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAG                         GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT
genomic: TCGCCTGCACCGCCTTCTTCCTCGCCTTCTCTGCCTACTCCCGTCGCCAGgtgtggcttt ... tgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaatgataagaatttcaaaagatttatcttacttttttctcatgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGATGTAGAAATTGATGGCCAACACATAG
                            atcttac  putative branch site (score: 3)
                         tttatcttactttttt  CT-rich tract
             aatttcaaaagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acactttatcagagaaaatcaaagaaaaaaagaactatgacagtacttgaatgataagaatttcaaaagatttatcttacttttttctcatgttgcatagGGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGATGTAGAAATTGATGGCCAACACATAG

- - - - - - - - aatcaaa
- - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - ttgaatg