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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccattttctgagattagttttttctgaatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaacctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 5
tccattttctgagattagttttttctg--aatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaacctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG
   |  |||| |  || ||||| ||     |||   |  ||   |||||||  |   |  ||||   | || | ||| |||||    | |||||| |  |||| ||  |||||||||||||||||||||||||||||||||||||||||||||| ||  | ||||||||||| | |||
-taaacttct-acttttgttttatcaacttatcatattttctgttattattctttcttgagaaatgcaatgttctaactgagtgcatctaaacctctattagACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAG

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 6
--tccattttctgagattagttttttctgaatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaacctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG
  |  |       | ||    ||  | |   ||  ||  ||   |  | |  || | | | |  || | || |  |||  |   |      || | ||| |||||||| |||||||||||||||||||||  |  | |||||||||||| | |||||  |  ||||  |||| | |||
tttataaagcaaaaaatggaattaatattcctcatctggtcagttggtgtaaatttttgt-agtcaaaatggtg-aataaaaattccatgcacattttgcagATCCTGGTGCAAGTGCTGATCTAGCAGTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 7
tccattttctgagattagttttttctgaatcgcctc--atcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaacctat-tgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG
 | | | | | ||  |    | || | |   || |   |||   | |||| |  |  | |    | | | | || || |   |   ||    | |||    |||||| ||||| |||||||||||||| ||  |||| |||||||||||||| || ||  | |||||  | |||| |||
-ctaatgtttcagtatgtcatattgtcatgtgcttttgatctcatgttatcttccatttttt--cttccgggttcaaatttattgcacttgtcttatgcacagATCCCGCTGCTAGTGCTGATCTAGCTGTAGTTCTAATGCAAGAAGGACTGGCACAAATCTTCCTTGTGGGCAGAAG

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 6
tccattttctgagattagttttttctgaatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaaccta--ttgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG
|   | ||||   |  |  |    |    |    |  |  |        ||   || | ||      |  ||  ||   |  | ||     |||  ||  |||||||||||||||||||||| |||||||  || | |||||||||||| | || ||  |  |||||||||| | |||
tatgtcttctattacaa--tgacaccattttattttgtattaggaaggctaaaagtctaaattcaggttcttacataatgcttaactccctctaaatttcagATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAG

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|19351008|gb|BM895540.1|BM895540
EST:     GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|19272449|gb|BM888705.1|BM888705
EST:     GAAATTTGGGATTGGTGAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     TGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: TGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|19351610|gb|BM896142.1|BM896142
EST:     GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|19351009|gb|BM895541.1|BM895541
EST:     GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|89251335|gb|DY623121.1|DY623121
EST:     GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
EST: gi|22491504|gb|BU051427.1|BU051427
EST:     GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTG                         ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG
genomic: GAAATTTGGGATTGGTTAGCACTTGAGACCATTCAGCAAGCATGTGgtatgcgatt ... cctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatctgtatgaaacatactgatttaattgagtctgaccaaacctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG
                  atactgatttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccattttctgagattagttttttctgaatcgcctcatcctctattatttatctgtatgaaacatactgatttaattgagtctgaccaaacctattgtagATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG