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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatagactgaaagtagttcatggaagatgacctcatatacggacacaaaaaataataagaaagcaccaaataagttgtgcaacacacgttctggatacacatacataatacagaaaaagagacgcttttcttataaattgttatttttctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAGTGCCAGATTCAGACGAAGAGTTCTTGCTGCATCCAGCAACAGTTAGACG

Basic information

species Zea mays
transcript GRMZM2G129208_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 12
gtaaatagactgaaagtagttcatggaagatgacctcatatacggacacaaaaaataataagaaagcaccaaataagttgtgcaacacacgttctggatacacatacataatacagaaaaagagacgcttttcttataaattgttatttttc-tgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAGTGCCAGATTCAGACGAAGAGTTCTTGCTGCATCCAGCAACAGTTAGACG
                                                            ||         || || | ||   |||  |      ||||    |   |  |    ||         || |  | ||   ||  | |||||| | ||| ||||||| ||||| || ||||| |||||||| |||| ||||||| |||||||||| ||||||||||| |||||||||||| |||||||||||||||| ||| |
------------------------------------------------------------agcttttgttcaaaaaat-gtattaca-gcaaaacagatatgtttctttttttaccaagtttttctcctgtaatgatgtgttaatctttttcattttgccagTTTCAACAGCAGTTTCCTATGATAGATCAATTAGAGCAATCCGAGTGAAAGTACCAGATTCAGATGAAGAGTTCTTGTTGCATCCAGCAACAGTCAGAAG

upper sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 11
gtaaatagactgaaagtagttcatggaagatgacctcatatacggacacaaaaaataataagaaagcaccaaataagttgtgcaacacacgttctggatacacatacataatacagaaaaagagacgcttttcttataaattgttatttttctgttgtc-agTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAGTGCCAGATTCAGACGAAGAGTTCTTGCTGCATCCAGCAACAGTTAGACG
                                                            |  || |  | || |  || ||          ||    |   | |      |       |   |    || | |||  || |  ||| ||  |  |||| ||| || ||||| ||  |||| |||| ||  || |||||||||||||||||||| ||||||||||| ||||||||| | |||||||| || || || |||||
------------------------------------------------------------atcaaactgccaacatattttggggttgttactccatttggccctgagc--tttgttccatttggtctttattttaacaaatactatcttctttctgtccagTGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAGTACCAGATTCAGAAGAAGAGTTCCTTCTGCATCCTGCTACTGTAAGACG
















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|32921765|gb|CF026577.1|CF026577
EST:     GAATCTTGGGGCATGTGTTGCTCAACAGTGTGCTAAAATCAGGCAACAAG                         TTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
genomic: GAATCTTGGGGCATGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAGgtaaatagac ... ctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
EST: gi|60400398|gb|DN233205.1|DN233205
EST:     GAATCTTGGGGCATGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAG                         TTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
genomic: GAATCTTGGGGCATGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAGgtaaatagac ... ctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
EST: gi|32920197|gb|CF025009.1|CF025009
EST:     GAATCTTGGGGCACGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAG                         TTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
genomic: GAATCTTGGGGCATGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAGgtaaatagac ... ctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
EST: gi|32921998|gb|CF026810.1|CF026810
EST:     GAATCTTGGGGCATGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAG                         TTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG
genomic: GAATCTTGGGGCATGTGTTGTTCAACAGTGTGCTAAAATCAGGCAACAAGgtaaatagac ... ctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatacagaaaaagagacgcttttcttataaattgttatttttctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAGTGCCAGATTCAGACGAAGAGTTCTTGCTGCATCCAGCAACAGTTAGACG
                                     ttatttttct  CT-rich tract
                      ttttcttataaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagactgaaagtagttcatggaagatgacctcatatacggacacaaaaaataataagaaagcaccaaataagttgtgcaacacacgttctggatacacatacataatacagaaaaagagacgcttttcttataaattgttatttttctgttgtcagTTTCTACAGCGGTGTCCTACGATAGATCCATTAAAGCAATCAGAGTGAAAGTGCCAGATTCAGACGAAGAGTTCTTGCTGCATCCAGCAACAGTTAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC