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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagtttacactgcttcactttatttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
----------------------------gtaccagtttac-actgc-ttcactttatttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
                             |  || |||   |   | | |   | || ||||    ||   |   ||      ||||  |  |  ||||| || || ||||||||| | ||||| ||||||||||||||||| ||||| ||||||||||
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG

upper sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
-------------------------------gtaccagttta-cactgcttcactttat-ttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
                                 |     ||| |||| | | |   ||| ||   |||   | ||||  |     |  | | |  || ||||| ||||| ||||||||| | ||||||||||| ||||||||||| ||||| || |||||||
gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaat-ttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG

upper sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 8
----------------------------------gtacca-gtttaca-ctgcttcactttatttatttttctttcctatca-tgaccccctaagtattat-attgaaatctacgtcaa--agCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
                                   ||  | ||| | | ||  || | ||  | |  |||| |    |   | |||     ||  |||||| |||   ||     |  |  |||||||||||||| ||||| |||| |||||||||||||| || ||||
gtaagtgcctcttttcatatattgtagctgaggaatatgatgttcatatctagttgaattactcttgttttgtgctatgctagtgaaatgatatatattattattattattatttttgagcagCTTGCGGAGGACTTGGGTACTGCACCAATATGGGTATTTAATAATG

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|32924623|gb|CF029435.1|CF029435
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     GTGGCATTACTGGACTGATGATGGGNC-TGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTGGCATTACTGGACTGATGATGGG-CTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|18654845|gb|BM499650.1|BM499650
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG
                          taagtattatattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccagtttacactgcttcactttatttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC