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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT

Basic information

species Zea mays
transcript GRMZM2G004528_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 5
gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
  || | || |||  |||||    | |||  ||||  |||   | |||     |    | |    || ||||||  ||| |  ||||||||| ||||||||||| ||||||||||||||||| |||||||| || ||||||||||| ||||| |||||||| || ||| |||||||||| || ||
--gtatgtaattttctgtgt----agagtagtatgcggtttattttctc----aggttcatggcttatttgtttactgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGT

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 5
---gtgtgtttagtttggtgtgttcccaaagttttatggtgtt-gcatctctgttcaaaaaacttattatacttgtttcatgtttgt-agGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
   |  || ||   ||  |||   ||| |    |||   |||| | || | || | |         ||    |||| |  |  |  | |||||||||||||||||| |||  ||  |||    |||| ||||| || |||||||||||||| |||||||| |||||||| ||  ||||||||||||||||
gttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACTTCAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTTGATTTTCTTGT

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G31450.2 (Glycine max), 3'ss of exon 5
gtgtgtt-tagtttggtgtgttcccaaagttttatggtgttgcatctctgt----tcaaaaaacttattatacttgtttcatgtttgt---agGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
||   || | | ||  | |  |      | || ||    ||  || | ||     | || ||| |  | |   ||| ||  |||||     ||||||||||||||| || |||||||  ||| |  |||| || || || ||||| |||||||| |||||||| |||||||| ||  |||| ||||| |||||
gttcattattgattattattattatgtgggtt-attaaattttatttatgcaaaataaataaattggtgaattttgctttgtgttttcgtcagGGCTGATTGATCTGGCCATCAAGAGGAACAGTTTGATTGGAGGAGATGACTTTAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTGGATTTCCTTGT

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgt---agGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
    ||||  | | ||    |   ||    | ||  || |  |||  | ||  |||   | | |    || ||    ||||||   ||| || |||||| | || |||| ||||||     |||||||||| || || ||||||||||| || |||||||||||||| ||| |||||||||| || ||
----gtttcatgtagttgagttttaatcactcat--tgatcaatcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgtttagtttggtgtgttcccaaa--gttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
  ||   ||  ||    | |  | | |  || |||  |   | ||  | | |  |  || |  ||| | ||| | | |    |  |||||| |||||  | || || ||||  |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| |||||
--gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatatta----tacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 4
-------gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttatt--atacttgtttca-------tgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
        |  ||||  ||||    ||||     |  | |  ||   || | |    | | | | || |||  |   | ||||||       || ||| |||  | |||||    ||| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || || || || ||||| ||
gtacagaattggttttttttgagaggttcgtgttgcataagagtaccgc-ttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT

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|31359455|gb|CD443812.1|CD443812
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32855391|gb|CD995072.1|CD995072
EST:     GGAAGGGGTGCCATTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32856301|gb|CD995982.1|CD995982
EST:     GGGGTGCCATTCAGCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32855713|gb|CD995394.1|CD995394
EST:     GGAAGGGGTGCCATTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|6637095|gb|AW261367.1|AW261367
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|211037209|gb|FK948218.1|FK948218
EST:     GGAGTGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACTACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|91871596|gb|EB401553.1|EB401553
EST:     CTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: CTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|13516068|gb|BG518344.1|BG518344
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|6527007|gb|AW216231.1|AW216231
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|6637051|gb|AW261323.1|AW261323
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32831002|gb|CD970680.1|CD970680
EST:     GGAAGGGGTGCCATTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32803449|gb|CD955685.1|CD955685
EST:     GGAAGGGGTGCCATTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|211029038|gb|FL245284.1|FL245284
EST:     CATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: CATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|6021328|gb|AW066256.1|AW066256
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         NGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|33098850|gb|CF058810.1|CF058810
EST:     GGAAGGGGTGCCATTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32921535|gb|CF026347.1|CF026347
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCCGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|31364344|gb|CD448699.1|CD448699
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32921566|gb|CF026378.1|CF026378
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|60346856|gb|DN213829.1|DN213829
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|21621348|gb|BQ619354.1|BQ619354
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|32920511|gb|CF025323.1|CF025323
EST:     GGAAGGGGTGCCATTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|211032313|gb|FK948194.1|FK948194
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCARAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGKGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
EST: gi|67029746|gb|CO458495.1|CO458495
EST:     GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTG                         GGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT
genomic: GGAGGGGGTGCCGTTCATCAATGGGAGCCCCCAGAACACTTTTGTGCCTGgtgtgtttag ... atgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT
                      aaaaaacttattatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG