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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataatcagtatgttgtgatctttataacctagtttgtcctccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA

Basic information

species Zea mays
transcript GRMZM2G172101_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 7
---------gtaataatca-gtatgttgtgatctttataacctagtttgtcctccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
         | ||   |||   || ||  |  | || | || | |     |   | |  | |||||||   ||| || | |||| ||  | |||||||| ||||| |||||| |||| |||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| |
gtagacatcggaagcttcacacatcttaagcaccttgttacat-gcggaactgtcttttgatgtctaatcatttcttcattgtctattatacagATTGGCCTACCGTACCAACTTGTCTCCATTGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 7
gtaataatcagtatgtt-gtg-atctttataacctagtt-tgtcct------ccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
|||   ||||| |  || ||  ||||| |  |||| |||   ||||       | |  | |||||||   ||| || | |||||||  | |||||||| ||||| || ||| |||| ||||| || ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| |
gtagagatcagaagcttcgtacatcttaagcaccttgttacatcctgaactgtcttttgatgtctaataatttcttcattgtccattatacagATTGGCCTACCGTATCAACTTGTCTCCATCGTGTCTGGTGCTCTTAATGATGCTGCAGCTAAGAAGTATGATTTAGAAGCATGGTTCCCTGCATCAAAAA

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 7
----------------gtaataatcagtatgttgtgatctttataacctagtttgtcctccctgagttgtctaaatttttatttaatgtccatc-ttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
                ||| |  |  || |    | |  || | | | |  |||  ||    | | |||| |    | | ||| ||| |   |   ||||| |    || || || ||||||||||||||||| ||||| ||| | ||||||||||| || ||||| |||||| | ||||||||||| || || ||  |  
ttgcgtttagattgatgtattggttggtctaacctaaa-ttgacatctttcttttcccaagtttatttgtttctcgtgtgattaaattttatttactgcagTTAAACCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCTTTGAATGATGCTGCAGCAAAGAAGTATGATCTAGAAGCATGGTTTCCAGCCTCTCAAG

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G29600.1 (Glycine max), 3'ss of exon 7
-----gtaataatcagtatgttg--tgatctt-tataacctagtttgtc---ctccctgagttgtctaaatttt---tatttaatgtccatct--tgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
     ||    ||   | | |||  || |||    |||  |   || |    |||||   ||| | |   | |    |  ||||  |  || |  ||||| |    || || || ||||||||||||||||| ||||| ||  | ||||||||||| || ||||| |||||| | ||||||||||| || || ||  |  
attgtgtgtagattgatgtattggttggtctgacttaaattgacttctttctctccccatgttttttgtttctcatgtgattaaattttatttactgcagTTAAATCTTCCCTATCAAGTTGTTTCCATTGTATCTGGTGCATTGAATGATGCTGCAGCAAAGAAGTATGATCTAGAAGCATGGTTTCCAGCCTCTCAAG

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv14s0128g00370.t01 (Vitis vinifera), 3'ss of exon 7
-----------gtaataatcagtatgttgtgatctttataacctagtt-----tgtcctccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
           | |        | || | ||||  ||||  | ||||      || |||   |          ||| |   |  | |  |  | || ||| |     | || || ||||||||| ||||||| ||||| ||  | |||||||| ||||| ||||| ||||||||||||| |||||||||||||||  |||
atgaaagaaatggatctgctcttgtgatatgatgattattccttagtgaagaatgcccttttttccgccctggaatgtaactccatttcctctattacagCTAAACATTCCCTATCAAGTTGTTGCCATTGTTTCTGGTGCCTTGAATGATGCAGCTGCAAAGAAGTATGATTTGGAAGGATGGTTCCCTGCATCCCAGA

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S142_120V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------gtaataatcagtatgttgtgatctttataacctagtttgtcctccctga--gttgtctaaatttttatttaatgtc-catcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
              |   ||      | ||| || || |       |||    || |   |||   |  | | | |  | |  |  | |    | |||||| | || || || || | ||| || ||||| |||||||| || ||||| |||  ||||||||||||||| |||||||| |||||||| || || || ||||
ctctttgtttctccgctttacatgaaaagtt-tgctcgtgtactattagaccatcttttgtgaccatgttatgactcatcaggttgtatgatgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGATAGTGCTGCTAAGAAATACGATTTGGAGGCATGGTTTCCAGCTTCCAAGA

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|71766798|gb|DR964735.1|DR964735
EST:     GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAG                         ATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT
genomic: GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAGgtaataatca ... catcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT
EST: gi|31352352|gb|CD436709.1|CD436709
EST:     GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAG                         ATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGTGCTCTTAATGAT
genomic: GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAGgtaataatca ... catcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT
EST: gi|78113530|gb|DV531921.1|DV531921
EST:     GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAG                         ATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT
genomic: GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAGgtaataatca ... catcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT
EST: gi|32932030|gb|CF036842.1|CF036842
EST:     GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAG                         ATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT
genomic: GGGAGATGCATGAAGAGATGCTAAAAAACTCAGAAGATTACTATAAGGAGgtaataatca ... catcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctagtttgtcctccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
                                           tccatctt  CT-rich tract
                   agttgtctaaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataatcagtatgttgtgatctttataacctagtttgtcctccctgagttgtctaaatttttatttaatgtccatcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG