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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCAGCAGCATCAAATCTTGGAAAGTTTGCAGCTACAGTTGAACAGAATCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattctatatacagtttcaatgaaatgtgttgtgttcctccgtttgtttcttgcttcttgcactgattattccctgttatttgtcctttttttcgag...

Basic information

species Zea mays
transcript GRMZM2G164352_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 4
AGAGCAGCAGCATCAAATCTTGGAAAGTTTGCAGCTACAGTTGAACAGAATCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattctatatacagtttcaatgaaatgtgttgtgttcctccgtttgtttcttgcttcttgcactgattattccct------gttatttgtcctttttttcgag
||| | || ||||||||||| ||||||||||| ||||| ||||||     |||||||||| | || || |||||||||||||| ||| | || || |||||||  |    | |  | | |  |||    || ||   |||| |  |||| ||  |      ||||   |   ||  ||      ||||||||| |  ||||     
AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatg---cgtatttgattccactctttgattgctatgatatgcatacacacttttctatttgagttatttgttcaattttct---
















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|32831601|gb|CD971279.1|CD971279
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|33091965|gb|CF051959.1|CF051959
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGACTTAACCCAAGATG                         ATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|21088918|gb|BQ401231.1|BQ401231
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|22473017|gb|BU037497.1|BU037497
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211520937|gb|FL382784.1|FL382784
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32940030|gb|CF044849.1|CF044849
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32830645|gb|CD970323.1|CD970323
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32938569|gb|CF043388.1|CF043388
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|26456172|gb|CA827755.1|CA827755
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCA
EST: gi|22935744|gb|BU572019.1|BU572019
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGGGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32847343|gb|CD987024.1|CD987024
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211194221|gb|FL384750.1|FL384750
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|19770363|gb|BQ035084.1|BQ035084
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32831720|gb|CD971398.1|CD971398
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTG
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTG
EST: gi|213188056|gb|FM186556.1|FM186556
EST:     TCATTTGAAGACAGAAATAATGTNNNTATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32829962|gb|CD969640.1|CD969640
EST:     ATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: ATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32851452|gb|CD991133.1|CD991133
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211356091|gb|FL413289.1|FL413289
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGNA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211150174|gb|FL390449.1|FL390449
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCAGCAGCATCAAATCTTGGAAAGTTTGCAGCTACAGTTGAACAGAATCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattctatatacagtttcaatgaaatgtgttgtgttcctccgtttgtttcttgcttcttgcactgattattccctgttatttgtcctttttttcgag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG