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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcccggtagaatccgtagttctaccatgccttttgccacatattacatgctgaaaaatttatccgagttcatcatctcttatctggtagcaatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 3'ss of exon 8
gcccggtagaatccgtagttctaccatgccttttgccacatattacatgctgaaaaatttatccgagttcatcatctcttatctggtagcaatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG
     |||    ||    |||    || | |  || |  ||  | |||       | |||    ||     | | ||  |  ||||| |||||||| ||||| || ||||||||| ||||||||||||| |||||| | |||||||||||||| ||||||||||||||||  ||||||
-----gtacgtgccacttttcccttattcttcatgtcggatgattcatat----gattttgcatga---tgtgagctggtgcctggtggcaatactgcagGAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCTGCATTATTTGAGGACCCAACATTCAAG
















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|4887369|gb|AI677468.1|AI677468
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|7162396|gb|AW520018.1|AW520018
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|60342201|gb|DN209174.1|DN209174
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|24934386|gb|CA452604.1|CA452604
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|71327463|gb|DR800349.1|DR800349
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|67022725|gb|CO451474.1|CO451474
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|7216381|gb|AW562503.1|AW562503
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|101393103|gb|EB818482.1|EB818482
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|60397958|gb|DN230774.1|DN230774
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|7238058|gb|AW573325.1|AW573325
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTC
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTC
EST: gi|74246091|gb|DT654005.1|DT654005
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|7204636|gb|AW559169.1|AW559169
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|60349847|gb|DN216820.1|DN216820
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|5740004|gb|AI947694.1|AI947694
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|211351874|gb|FK984289.1|FK984289
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|76920121|gb|DV168019.1|DV168019
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|76292512|gb|DV032080.1|DV032080
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|211216297|gb|FL460273.1|FL460273
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|60342528|gb|DN209501.1|DN209501
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|71759931|gb|DR957868.1|DR957868
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|14244899|gb|BG842837.2|BG842837
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|88753851|gb|DY537992.1|DY537992
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTTTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
EST: gi|7145161|gb|AW506642.1|AW506642
EST:     GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG                         GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT
genomic: GGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAGgtgtgtgcct ... aatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgctgaaaaatttatccgagttcatcatctcttatctggtagcaatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG
     tgaaaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcccggtagaatccgtagttctaccatgccttttgccacatattacatgctgaaaaatttatccgagttcatcatctcttatctggtagcaatacttcagGATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT