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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctcctagttgttttcgtgcatttctcgtgcttactcaaaacatgcagctattctgcttggtatattaactacattctaaatcgacatgttcataatgattttattattgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATCATTCCGTGGAGAATTTGAG

Basic information

species Zea mays
transcript GRMZM5G806449_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 3
gtaagcatctcc----tagttgttttcg--tgcatttctc-------gtgcttactcaaaacatgcagctattctgcttg------------gtatat------taactacattctaaa-tcgacatgttcataatgattttattattgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATCATTCCGTGGAGAATTTGAG
|||||||||| |    || |||| | ||  | |||||||         |||||  | |  |  |  | | | ||| ||              | || |      |  || ||| |||||  |  |||| |||| ||  |     | |||| |||| || |||||||||||||| || |||||||||||||| ||||||||| |||| ||||| ||||||||||||
gtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtaca--tgttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG
















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|211339792|gb|FK980808.1|FK980808
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211339790|gb|FK980806.1|FK980806
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACMTGGTGGGAC                         TTGCGTGATACGTGGTTGCGTATCTGAAAAGATACTCGT
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGT
EST: gi|211339794|gb|FK980810.1|FK980810
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|33942501|gb|CF349101.1|CF349101
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211339793|gb|FK980809.1|FK980809
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211337407|gb|FK980805.1|FK980805
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211339796|gb|FK980812.1|FK980812
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211337405|gb|FK980803.1|FK980803
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|40485831|gb|CK394761.1|CK394761
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|33942302|gb|CF348902.1|CF348902
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGCGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|148945432|gb|EC890664.2|EC890664
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211337397|gb|FK980795.1|FK980795
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211337400|gb|FK980798.1|FK980798
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|148969995|gb|EE020910.2|EE020910
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|211337398|gb|FK980796.1|FK980796
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGT
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGT
EST: gi|148960879|gb|EE011558.2|EE011558
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
EST: gi|33101538|gb|CF061498.1|CF061498
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCT
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCT
EST: gi|111991059|gb|EE331961.1|EE331961
EST:     CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC                         TTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC
genomic: CTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatct ... attgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattaactacattctaaatcgacatgttcataatgattttattattgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATCATTCCGTGGAGAATTTGAG
                                              ttgtcct  CT-rich tract
                         atgttcataatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatctcctagttgttttcgtgcatttctcgtgcttactcaaaacatgcagctattctgcttggtatattaactacattctaaatcgacatgttcataatgattttattattgtcctagTTGCGTGATACGTGGTTGCGTACCTAAAAAGATACTCGTGTATGGTGCATCATTCCGTGGAGAATTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA