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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa...

Basic information

species Zea mays
transcript GRMZM2G112865_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 5'ss of exon 5
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttg-gcattgttacatccaaa-----
  | |||||||| || ||||| ||| | ||  |||| |||||||| |||||||||||||| || ||||||||||| ||||||  |||| |   |||  || ||  |    ||| ||    |||   |  |     |||| |  | || |  | |||| ||  ||   |    |  ||       
GAACCGAGCTGGTGGGTACACCAGACTATTGCGAACTAGGATACGAGTTGGTGATGCTGCACCGATGGCATACATTGAgtaagcttctct---tatgatttttaaaatggaaaattg--atcagtgacctttccattgg-gttattagtcagttttttttttgcggggaattagtcagttttgt

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g38580.2 (Oryza sativa), 5'ss of exon 5
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaa---cattctttatctat-atttcttggaga---taaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa
|||||||||||| || || |||||| |  |  | || |||||||| ||||| |||||||| |||||||||||||| |||||      ||| || | ||  ||  || ||| |    |||||||||  |   || | | |    ||   |  | || ||   |    ||      ||         
AGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGAgtatgtcttttccttgtttaccataactaggaaaattcaaaatttacatttgaatttctcattgctgtttgttgcaagtgttctggtctgatgcaattcg-------

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 5
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaa---cattctttatctat-atttcttggaga---taaaatttaccgtcatatatttaa----aacttggagggagtaattggcttttcttggcattgttacatccaaa-------------------------------------------------------------------------
|||||||||||| || || |||||| |  |  | || |||||||| ||||| |||||||| |||||||||||||| |||||      ||| || | ||  ||  || ||| |    |||||||||  |   || | | |       |||  |  |||  |  | | |  |     | |||   | || |                                                                         
AGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGAgtatgtcttttccttgtttaccataactaggaaaattcaaaatttacatttgaatttctcattgctgtttgttgcaagtgttctggtctgatgcaattcgttttcttcatattcatttcaaagttgtaactattggactaacagacaagtacccttcatgttctattctattcatccgtttcag

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT5G64650.1 (Arabidopsis thaliana), 5'ss of exon 5
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaaca----ttctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa
|||| ||||||| || |||||||||||| |  | ||  | || ||||||||||||||||| |||||||| || ||||||||| |    ||  || ||| ||||  ||  |    ||   ||  |   |  | || |   || |    ||| |          | |    || || ||   | 
AGATAGAGCTGGTGGATACACAAGAATGCTTCGTACTCGCATTCGTGTTGGTGATGCTGCCCCAATGGCCTATATCGAgtaaaacaagtttcttttctttattctttttaacagaagcatattgaattcgagtttag-tttagtcacagttac--aacaaaatggatgatgctatatttta-

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 5'ss of exon 5
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagata--aaatttaccgtcatatat-----ttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa----------------------------
|||| ||||||| || ||||||||| || || | ||  | ||||| ||||||||||||||||| ||||| || ||||||||| | |  ||   | | ||| |  |   |      |||||  |||||| |     ||| | |    | | |||  |     |||    || || |      | ||                            
AGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGAgtaaaactagtttcttttctttatcagtctttctggttttacattcatatctccatgttagatcaaataagaagtgttaatgatttggaagctttctggtgaactaatttggtcgatacttgatactttggatag

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|33099991|gb|CF059951.1|CF059951
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|37393499|gb|CF634015.1|CF634015
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGACAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|211239658|gb|FL451920.1|FL451920
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|60353121|gb|DN220094.1|DN220094
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|22490485|gb|BU050408.1|BU050408
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAAC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAAC
EST: gi|21987795|gb|BQ779323.1|BQ779323
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|32929716|gb|CF034528.1|CF034528
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|60397912|gb|DN230728.1|DN230728
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|87151864|gb|DY396653.1|DY396653
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC
EST: gi|18965108|gb|BM661397.1|BM661397
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC
EST: gi|32909297|gb|CF014109.1|CF014109
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|50337603|gb|CO532729.1|CO532729
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|22545985|gb|BU098344.1|BU098344
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa

- - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT