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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatcagaactgcagtttttatttgcttttatcttgacagcggaggaatcaggataccattatttgctaatcttccttaatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCTGCACAGCAATTTGTTAGGGCTGAGATGCTTCCAAGTGGGTATTTAGTGC

Basic information

species Zea mays
transcript GRMZM2G042250_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 8
--gtatgtgatcagaactgcagtttttatttgcttttatcttgacagcggaggaatcaggataccattat--ttgctaatcttccttaatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCTGCACAGCAATTTGTTAGGGCTGAGATGCTTCCAAGTGGGTATTTAGTGC
   | | ||| ||  |   | ||||| |           |   |||  |   |  |||   |    |||   |||||||| |||||  ||||||||||||||||||||||| || | |||||| || |||||||||| ||| || ||||| ||||||| ||| || || || |||||||||||||| ||  | || |
gtatgtatgaacatgaacactgttttca-----------ccccacaatga--gtctcaatgtgatgttacccttgctaatattcctccatctccaagGTCTGTGAGAGATCTTTAAGTGGTTCAGGGGGCGGTCCAAGTGCTGCCTCTGCTCAGCAATATGTGAGAGCGGAAATGCTTCCAAGTGGATACCTGGTTC
















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|211157806|gb|FL365669.1|FL365669
EST:     ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTG                         GTCTGTGAGAGATCCTTGTNTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
genomic: ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTGgtatgtgatc ... aatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
EST: gi|71422277|gb|DR805676.1|DR805676
EST:     TTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTG                         GTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
genomic: TTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTGgtatgtgatc ... aatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
EST: gi|211282791|gb|FL192982.1|FL192982
EST:     ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTG                         GTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
genomic: ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTGgtatgtgatc ... aatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
EST: gi|211263135|gb|FL355114.1|FL355114
EST:     ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTG                         GTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
genomic: ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTGgtatgtgatc ... aatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
EST: gi|211357660|gb|FL143935.1|FL143935
EST:     ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTG                         GTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
genomic: ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTGgtatgtgatc ... aatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
EST: gi|60340950|gb|DN207923.1|DN207923
EST:     ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTG                         GTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT
genomic: ACTTTTGGACGTTGCGATACACGACAACAATGGAAGATGGCAGCCTTGTGgtatgtgatc ... aatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacagcggaggaatcaggataccattatttgctaatcttccttaatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCTGCACAGCAATTTGTTAGGGCTGAGATGCTTCCAAGTGGGTATTTAGTGC
                                     tcttccttaatctcc  CT-rich tract
                         attattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgatcagaactgcagtttttatttgcttttatcttgacagcggaggaatcaggataccattatttgctaatcttccttaatctccaagGTCTGTGAGAGATCCTTGACTGGTTCTGGAGGCGGTCCAAATGCAGCTTCTGCACAGCAATTTGTTAGGGCTGAGATGCTTCCAAGTGGGTATTTAGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG