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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactggagaacattcactaacattcatgtccttggttttcttgcttctaaaacatggttgctttgcttgtaatttacacag

Basic information

species Zea mays
transcript GRMZM2G069758_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069758_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 11
GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactggagaacattcacta---------------------acattca----tgtccttg----gttttcttgc--ttctaaaac-------atggttgctttgcttgtaatttacacag
|| ||||||||||| |||||||| || ||||||||||||||||||||  || |  ||  |  || || |                     |  || |    ||  |||      ||||||||   || ||||||       | | |  |||||||| | ||||  ||||
GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtcccagatgaactttaccatttttttctcgaaagcagatgaagtttaccattgctcttatagaattttcttgtcattttaaaaccacttctaagttctctttgcttttgatttgtacag
















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|18166331|gb|BM336170.1|BM336170
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|33097992|gb|CF057952.1|CF057952
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     GGAACTGGAGATTTGGCAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|8102609|gb|AW927412.1|AW927412
EST:     AGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: AGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactggagaacattcactaacattcatgtccttggttttcttgcttctaaaacatggttgctttgcttgtaatttacacag

- -  TGGAGA
- - - GGAGAT
- - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - GATGGA