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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttctctatggttcttgagatctaattattgcaatgtcttctgggtggactaaatatttttcatgcttgatgcgttggtttcatgtgttgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG

Basic information

species Zea mays
transcript GRMZM2G098815_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098815_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 2
tacttctctatggttcttgagatc--taattattgcaatgtcttctgggtggacta--aatatttttcatgcttgatgcgttggtttcatgtgttgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG
|| |  | |||| ||      ||   | | |||   |  ||||| ||  |  | |   | | ||| |||||||||| |   | |||| ||   |  ||| ||||||||||||||||||||| ||||| ||||| |||||||| ||||||||||| || ||||||||| | |||||||| | ||| |  |||
taata-tatatgttttgcagaattatttactatgttagagtcttatgtttctattgttattgtttatcatgcttgaagttatagttttat---tatatcaacagGCAGCCTGTGATGAAACATCAGAAAAATCGGAACGGGCATTTGTCCAACTTTTGTTGACTTCAGCAAGTGGAAACAATAACATTGAG
















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|211052432|gb|FL214543.1|FL214543
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|71438169|gb|DR819219.1|DR819219
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAC                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|71765717|gb|DR963654.1|DR963654
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|78117671|gb|DV536058.1|DV536058
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|148952745|gb|EC898726.2|EC898726
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|71438316|gb|DR819366.1|DR819366
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|211052429|gb|FL214540.1|FL214540
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGT
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGT
EST: gi|74245464|gb|DT653378.1|DT653378
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|71433709|gb|DR814759.1|DR814759
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|76926415|gb|DV170849.1|DV170849
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|149082609|gb|EE171808.2|EE171808
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|50336738|gb|CO531864.1|CO531864
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|89253146|gb|DY624932.1|DY624932
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|211052431|gb|FL214542.1|FL214542
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|211052434|gb|FL214545.1|FL214545
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|149005336|gb|EE039887.2|EE039887
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGGGATGAAACGTCACA-AAACTCAGAAC
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAA-TCAGAAC
EST: gi|211052435|gb|FL214546.1|FL214546
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTT
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTT
EST: gi|91873215|gb|EB403172.1|EB403172
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|149076111|gb|EE164690.2|EE164690
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|14245049|gb|BG873631.1|BG873631
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|211052430|gb|FL214541.1|FL214541
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|211052428|gb|FL214539.1|FL214539
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAWT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTTCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|78120056|gb|DV538440.1|DV538440
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
EST: gi|148960798|gb|EE011460.2|EE011460
EST:     AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAAT                         GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA
genomic: AGAGTTATTCGCCGCAGACAGCAAATCCATATATTCCTATATTGTTAAATgtaagtggta ... tgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggactaaatatttttcatgcttgatgcgttggtttcatgtgttgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG
     actaaatatttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttctctatggttcttgagatctaattattgcaatgtcttctgggtggactaaatatttttcatgcttgatgcgttggtttcatgtgttgatctacagGCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA