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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaacatatatattcttcctgcgacaggcacgaacatgcatgtgttcaatagcacagatgtgatgatatgactgtcaccatgtcttttag

Basic information

species Zea mays
transcript GRMZM2G300348_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 5'ss of exon 4
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca-tatatattcttcctgcgacaggcacgaac-atgcatgtgttcaatagcacagatgtgatgatatgactgtcaccatgtcttttag--------
|| ||||||| || |||||||||||||| || ||||||||||| |||||||| || ||||| ||||| ||||| || |||||||| || |||||||||||||||||  || || |     || |    |  | ||  | |  |  |   |       ||| | || |  |    |||   | |   |   |||||         
CACCCGAGTCGAAGGCAACAACTGAAAGTGTGTACAGTGCTGCTTTGGCTCTCGGCATTGCAAACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtcaatacagtggttttcactaatggtcataagctgtagaacagaatgtcggcatatatatagttcactgatcctaatacttcattttattttcacag

upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G40720.1 (Glycine max), 5'ss of exon 5
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaacatatatattct-tcctgcgacaggcacgaacatgcatgtgt-tcaatagcacaga--tgtgatgatatgactgtcaccatgtcttttag---
|| |  | ||  |||| ||||| || || ||||||| |||||||||||| || |||||||| || || || || ||||||||| | ||||||||||||||||||||  ||||  || |   |  ||           |   | |     | | |  | || |    |   |  || |||   | ||     |  |||    
CACCAAATTCAGAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGAATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtc-cataactactgagtattgatgtttatttaagtcttcggaaatattaggaacaaaatacttctagaatgtgaagtttacttctcccattatcac

upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 5
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagt-----aacatatatattcttcctgc-gacaggcacgaacatgcatgtgttcaatagcacagatgtgatgatatgactgtcaccat-gtcttttag
|| |  | ||  |||| ||||| || || ||||||| |||||||||||| || || ||||| || || || || ||||||||| | ||||||||||||||||||||     |  ||  || ||    || | || |     | |     ||   |  |  |    |  | |  |  |   | | ||||||| ||  | |  
CACCAAATTCCCAAGCCACAACAGAGAGTGTATACAATGCTGCCTTGGCCCTAGGCATTGCAAATCAGCTAACCAACATACTCAGAGATGTTGGAGAGGAgtaagtccataactatcgatgtttactcttcagaaatatttggaacaaaatacttgtagaatgtgaagtttacttctcccattatcaccattgtggtgtt-

upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 5'ss of exon 5
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca---tatatat---tcttcctgcgacaggcacgaacatgcatgtgttcaatagcacagatgtgatgatatgactgt--caccatgtcttttag
|| | || ||  | ||||| || || || || || |  || ||||||||  | || || || || || || || ||||||||| ||||||||||||| |||||||||| |   |||| |    |     || | |     |  | |||| |   |  |  || | | |  ||   | |  | ||   ||  |      ||  
CACCTGAATCACAGGCAACCACGGAGAGTGTCTATAAGGCAGCCTTGGCATTAGGGATCGCAAATCAGCTGACTAACATACTCAGGGATGTTGGAGAAGAgtaagtaaaaagctataaaaaaataactgtgtgcctatgtcacatatgcttccctagaggag-agaaaaatggataaacaaatgaaacattagaaaacttg-

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|32849860|gb|CD989541.1|CD989541
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|60344179|gb|DN211152.1|DN211152
EST:     GAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: GAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|149008705|gb|EE040899.2|EE040899
EST:     ACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: ACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|6827537|gb|AW331180.1|AW331180
EST:     CTAGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|12046181|gb|BF728320.1|BF728320
EST:     TAGGAATTGCGATCCATTTTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: TGGGAATTGCGAACCA-ACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|32920900|gb|CF025712.1|CF025712
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|71444099|gb|DR825149.1|DR825149
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTT---GA-GA                         -G--AG-A-AGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|60338830|gb|DN205803.1|DN205803
EST:     CTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|22521337|gb|BU080148.1|BU080148
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|78104639|gb|DV523057.1|DV523057
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|50325755|gb|CO520881.1|CO520881
EST:     GGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: GGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|78179163|gb|DV549536.1|DV549536
EST:     CTAGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|148946927|gb|EC892211.2|EC892211
EST:     ATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: ATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|32921193|gb|CF026005.1|CF026005
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|32849806|gb|CD989487.1|CD989487
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|32921725|gb|CF026537.1|CF026537
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|32795287|gb|CD947523.1|CD947523
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|32923712|gb|CF028524.1|CF028524
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|148958127|gb|EC904325.2|EC904325
EST:     TGGGAA-TGCGGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: TGGGAATTGC-GAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|71775306|gb|DR973184.1|DR973184
EST:     CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTTCCACAAGATGAGCTTGCACAGGCAGG
genomic: CTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
EST: gi|149075799|gb|EE164332.2|EE164332
EST:     TACTCCGGGATGTTGGAGAGGA                         TGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG
genomic: TACTCCGGGATGTTGGAGAGGAgtaagtaaca ... tgtcttttagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCGAGTCTAAAGCAACAACTGAAAGCGTATACAGTGCTGCCTTGGCTCTGGGAATTGCGAACCAACTCACGAACATACTCCGGGATGTTGGAGAGGAgtaagtaacatatatattcttcctgcgacaggcacgaacatgcatgtgttcaatagcacagatgtgatgatatgactgtcaccatgtcttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA