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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaattgctatactcacccatttgccagttaggttgtgttgttttacttataggagatgtttgtttttgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAGCGTGATGGTGAGATTAGGAAAGCTGCCCTTAATACGCTTGCAACAGCCT

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 37
---------gtctgaattgctatactcacccatttgccagttaggttgtgttgttttacttataggagatgtttgtttttgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAGCGTGATGGTGAGATTAGGAAAGCTGCCCTTAATACGCTTGCAACAGCCT
          |   |    |  |  |  |||  |||  | || |  | | |||| |  | | |   |  | ||| |||    |  ||||||| |||| ||  ||||||| ||||||| ||| || ||| | |||||||| ||||||||||| ||  |||||||||| |||||||| ||||| || || |
gtacgtatcattctatcgtccttttttcccctcttgataattgg--tatattgtctctcgtttcacacttctttttttcctccttgcagGTTAGTGGTTTACTGAAAAATTTGCCATCTGTAGCGGCATTAACAGCAGAACGTGATGGTGAAATCCGGAAAGCTGCTCTTAATACACTTGCCACTGCAT

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 8
gtctgaattgctatactcacccatttgccagttag-gttgtgttgttttacttataggagatgtttgtttttgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAGCGTGATGGTGAGATTAGGAAAGCTGCCCTTAATACGCTTGCAACAGCCT
   |  | |     |||    | ||  |   || | ||| | |     |||| |   |   | ||   |||  |    ||| |||||||     | |||   ||||   | ||||||    |||||||||||||||||||||| ||||||||||||||  | ||||| || || ||||  |
--gtacaatagagaactttttctttgacttttttgagttttttcaggatactgacctg---ttttcaatttgtttcaacagATTGGTGGACAATTAAAATCTTTGCAGGTGGTTGCAAGCTTGACAGCAGAGCGTGATGGTGAAATTAGGAAAGCTGCTTTAAATACACTGGCTACAGGTT
















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|28909669|gb|CB331043.1|CB331043
EST:     TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAG                         GTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAG
genomic: TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAGgtctgaattg ... tgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAG
EST: gi|4730484|gb|AI649650.1|AI649650
EST:     TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAG                         GTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAG
genomic: TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAGgtctgaattg ... tgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAG
EST: gi|211104805|gb|FL044858.1|FL044858
EST:     TTATTGGATACTTCATTGACCATCATGGGGACTGAGG                         GTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGA
genomic: TTATTGGATACTTCATTGACCATCAT-GGGACTGA-Ggtctgaattg ... tgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGA
EST: gi|166468088|gb|EG161712.1|EG161712
EST:     TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAG                         GTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGC
genomic: TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAGgtctgaattg ... tgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGC
EST: gi|32826124|gb|CD965802.1|CD965802
EST:     TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAG                         GTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAG
genomic: TAGAATGTGTTGATATTATTGGATACTTCATTGACCATCATGGGACTGAGgtctgaattg ... tgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccagttaggttgtgttgttttacttataggagatgtttgtttttgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAGCGTGATGGTGAGATTAGGAAAGCTGCCCTTAATACGCTTGCAACAGCCT
                                     tttgttttt  CT-rich tract
                ttgttttacttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgaattgctatactcacccatttgccagttaggttgtgttgttttacttataggagatgtttgtttttgtcacgcagGTTGGTGGGTTGATGAAAAACTTGCCATTTGTTGCAGCACTGACAGCAGAGCGTGATGGTGAGATTAGGAAAGCTGCCCTTAATACGCTTGCAACAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC