Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagttcatgtttctttctgatactgatgtttggatgctgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag

Basic information

species Zea mays
transcript GRMZM2G376727_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g01307.1 (Oryza sativa), 5'ss of exon 4
GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagttcatgtttctttctgatactgatgtttggatgctgtttctggtgctacct----ctgcatg-gaaatctgaatatgctctcatactatgttcag
|||||||| ||||| |||||| |  |||| ||| |||| |||||||| | ||| || ||||||||||||||||||||||||  ||||||||||||  |||| ||||   | |  || | |||| || ||||   |||||||||| || | ||  |     | |  |  ||| |||  || | ||||| |  |  ||||||
GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGGgtaagtaattgtgccattgcatgtacattctagtctgtttcgctctatgatcctaatgtgctgatgctgtttatgtttctggcatgcgccgtgtatgaattcttgatgttctctccttgttggttcag

upper sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G05530.2 (Glycine max), 5'ss of exon 4
GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc--atgccattgcatgcgcattgta---gttcatgtttctttctgatactgatgtttggatgctgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag
||||| || ||||||||||| || ||  ||||  ||||  |||| |||| ||||||||||||||||||||||||| ||   |  || |  |  | ||    ||  |    |   | |   || || ||  |||   | | ||| |  || | ||  |         |       || |                      
GAGGCATATTCAACTCCCATATTGCCTTTGGACGTTCTTTCTGATAGACCTCCTGAGAAGAAGTTTGAATGGGTATgtttccttatactttaacttgacagttacatgaatcagtatcaattgcttatgttga--ctggcatgttactttttgttttcatgtattctacttggttgga----------------------

upper sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G27250.1 (Glycine max), 5'ss of exon 4
GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagtt-catgtttc--tttctgatactgatgt-ttggatgctgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag
||||| || ||||||||||| || ||  ||||| ||||  |||| |||| ||| |||||||||||||||||||||  |  || ||    | | ||  | |   |||| ||||  ||  | ||   | ||  | | |||  ||   | | |  |  |   | | |||| |  |||   |    |  | |  |||  ||||
GAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatt-tcctgta--tacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgtttt-catgtat-tctacttggtttgacctgatat-ctcag

upper sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G27250.2 (Glycine max), 5'ss of exon 3
----------------------------GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagtt-catgtttc--tttctgatactgatgt-ttggatgctgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag
                            ||||| || ||||||||||| || ||  ||||| ||||  |||| |||| ||| |||||||||||||||||||||  |  || ||    | | ||  | |   |||| ||||  ||  | ||   | ||  | | |||  ||   | | |  |  |   | | |||| |  |||   |    |  | |  |||  ||||
TTATTGTAGTAGTTTTTTTCCCTATTAGGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGGgtatatt-tcctgta--tacttgaacttgacagttacatgaatcaatatcaattgcttttatgttgactgacatatttactttttgtttt-catgtat-tctacttggtttgacctgatat-ctcag

upper sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G05530.1 (Glycine max), 5'ss of exon 4
GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagttcatgtttctttctgatactgatgtttggatgc-tgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag
||||| || ||||||||||| || ||  ||||  ||||  |||| |||| ||||||||||||||||||||||||| ||   | |    ||  |   | |  ||        |   | ||   | || |||||     || |||| ||  |  |     || ||   |   ||  |   |   |||   |       
GAGGCATATTCAACTCCCATATTGCCTTTGGACGTTCTTTCTGATAGACCTCCTGAGAAGAAGTTTGAATGGgtatgtttccttatactttaacttg-acagttacatgaatcagtatcaattgcttatgttgactggcatgttactttttgttttcatgtattcta-cttggttggaccgacatctcag------

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|211340832|gb|FL479597.1|FL479597
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|15053451|gb|BI358996.1|BI358996
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|7135675|gb|AW498208.1|AW498208
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|15590113|gb|BI674729.1|BI674729
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|21987232|gb|BQ778760.1|BQ778760
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|211130311|gb|FL066378.1|FL066378
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|32828788|gb|CD968466.1|CD968466
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|60354184|gb|DN221157.1|DN221157
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|15215431|gb|BI431279.1|BI431279
EST:     TGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|30706031|gb|CD059006.1|CD059006
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|15590464|gb|BI675080.1|BI675080
EST:     GAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: GAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|87156435|gb|DY401224.1|DY401224
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|60347341|gb|DN214314.1|DN214314
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|32829808|gb|CD969486.1|CD969486
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|149106143|gb|EE291820.2|EE291820
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|60347158|gb|DN214131.1|DN214131
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|31611983|gb|CD568605.1|CD568605
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|38671702|gb|CD219303.2|CD219303
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|74243940|gb|DT651854.1|DT651854
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|78081691|gb|DV510103.1|DV510103
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|7137614|gb|AW499182.1|AW499182
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|76285099|gb|DV024667.1|DV024667
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|211354953|gb|FL243593.1|FL243593
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|8930280|gb|BE225044.1|BE225044
EST:     GCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: GCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|9255123|gb|BE345591.1|BE345591
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|60346405|gb|DN213378.1|DN213378
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|78080233|gb|DV508645.1|DV508645
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|78107599|gb|DV526017.1|DV526017
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|5006027|gb|AI712089.1|AI712089
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|24769483|gb|CA404612.1|CA404612
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|211130310|gb|FL066377.1|FL066377
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|15545702|gb|BI643496.1|BI643496
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|24765720|gb|CA400879.1|CA400879
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|37377085|gb|CF625114.1|CF625114
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|78080443|gb|DV508855.1|DV508855
EST:     TCCCCCTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|211379488|gb|FL165247.1|FL165247
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|16919381|gb|BM074163.1|BM074163
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|60356569|gb|DN223542.1|DN223542
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|89249519|gb|DY621305.1|DY621305
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|37383348|gb|CF628683.1|CF628683
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|8666106|gb|BE186922.1|BE186922
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|15590463|gb|BI675079.1|BI675079
EST:     TCCCCCTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG
EST: gi|60355754|gb|DN222727.1|DN222727
EST:     TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG                         GCTAAG
genomic: TCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatc ... ctatgttcagGCTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGgtaagtaatcatgccattgcatgcgcattgtagttcatgtttctttctgatactgatgtttggatgctgtttctggtgctacctctgcatggaaatctgaatatgctctcatactatgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT