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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtactttactgccctcagttcaattctgcaactgttacctatataatggtggcttgctcatattatagaaattgaaaaaaacatttgttttaattgtggcattctttattgtgacccttggttaattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG

Basic information

species Zea mays
transcript GRMZM2G175419_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175419_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
---------------------gtatgtgtactttactgccctcagttcaattctgcaactgttacctatataatggtggcttgctcatattat-agaaattgaaaaaaacatt-tgttttaattgtggcattctttattgtgacccttggtta--attgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG
                     || | | || |    |    | | |||||||    |  | ||  ||  | | |||   || |    |  | | || |||| |     | ||  ||   | |||   |  ||  ||  |  |    || ||||  | |      ||||| || ||||| || || |||||||||||||||   || ||||| |||||  |||| || |||||||| || |||||||| |||||||| ||||||
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG

upper sequence: GRMZM2G175419_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtatgtgtactttactgccctcagttcaattctgcaactgttacctatataatggtggcttgctcatat---tatagaaattgaaaaaaacat----ttgttttaattgtggcattctttattgtgaccct-tggttaattgcaaa-acagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG
             || ||| | |   |  | |   ||    ||     ||  |   |||  | |  |    | || || |   ||||||| |   |  | | ||    ||     |||    |||| |  |  |  |  | |    ||||||  |   ||||||||||||||| ||||| |||||||||||||||   || ||| || ||||  | ||  | |||||||| || || ||||| |||||||| ||||||
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
















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|37421775|gb|CF648589.1|CF648589
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|78109291|gb|DV527707.1|DV527707
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|15208745|gb|BI430629.1|BI430629
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|21809627|gb|BQ667945.1|BQ667945
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|76290330|gb|DV029898.1|DV029898
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|32795893|gb|CD948129.1|CD948129
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|60354503|gb|DN221476.1|DN221476
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
EST: gi|94473189|gb|EB702147.1|EB702147
EST:     AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         AAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC
genomic: AATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgtgtac ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgttttaattgtggcattctttattgtgacccttggttaattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG
      ttttaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtactttactgccctcagttcaattctgcaactgttacctatataatggtggcttgctcatattatagaaattgaaaaaaacatttgttttaattgtggcattctttattgtgacccttggttaattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG