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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag

Basic information

species Zea mays
transcript GRMZM2G017525_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag
|||||| ||||||||||||||||| |||||| ||||||||||||| |||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||||||||| |||||       || |||  | |     |  ||   ||||   || ||| | ||      | | | |||| | ||| ||| | | | ||  | | ||
GCTCACTCAGACTGTCAGAGAGCTCGAAGAAGCTGTTCTTGCTGGAGGTGCAGCTGCAAATGCTGTGAGAGACTATCAGCGCAAAGTCCAGGAGATGAATgtaatgcatga-------tgccctgagcacacgttcctgatgtttattctacctaatagaatg--gtaattgatgccaattt-aca-cttatgctgatgtcag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaa----tcctgatgtccttggaaatgcatta--tgcgttttaggatat-ctacttgagcaccatgactaatgcaagttttacaacgtttcct----attcttag-
|||||| || ||||| ||||||||||||||  |||| ||||| |||||||||||||||||||| || || || || |||||||||||||| || |||||||||||   ||||            |  |   |    ||||   |   || | |  | | || | |       | ||  |     | |||| ||  ||||  |    ||||||   
GCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCCGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctcta-gttaagatcatatttatttttgcacggtttatttgacattctttag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaat-gcaagttttacaacgtttcctattcttag---------
||| || || || || ||||| ||||||||  |||| ||||| ||||||||||| ||||||||||| ||||| || || |||||| |||| || |||||||||||   | |  | |     | ||     |  | | ||  |  |     ||    ||||   ||||  ||||  |||  ||||    | |    | || | |          
GCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCAAATGCTGTGAGAGATTATCAACGGAAATTTCAAGAAATGAATgtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattga---ccatagctaaaagcatcttttgttgcatgatttgttttgatactatatag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatc-tacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag-------
||| || || || || ||||| ||||||||  |||| ||||| ||||||||||| || |||||||| ||||| || || ||||||||||| || |||||||||||   | ||   |     | ||     |  | | ||  |  |    |||   |||    ||||   |   ||   | || |   | | ||  | ||   |        
GCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCCAATGCTGTGAGAGATTATCAACGGAAAGTTCAAGAAATGAATgtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaa---tcctgatgtccttggaaatgcattatgcgtt-----ttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcct----attcttag-
|||||| || ||||| ||||| ||||||||  |||| ||||| ||||||||||| |||||||| || || || || |||||||||||||| || ||||||||||    | ||   || | |     ||  || | |  | ||| ||     | |  ||||  |||  ||    | ||  |     | |||| ||  ||||  |    ||||||   
GCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAGGTGGTGCAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagt--taagatcatatttatttttgcatggtttatttgacattctttag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 5'ss of exon 7
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatc-----ctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag
| | || ||||| ||  | ||||| |||||| ||||||||||||||||| |||| |||||||| || ||||| |||||| ||||| |||| || ||||||||||||  | |||       | |   |||    |    |||       ||    |    | |  |   |  ||   |    |  | |  | |    |||| |  ||||
GTTTACCCAGACCGTACGGGAGCTTGAAGAAGCTGTTCTTGCTGGTGGTACAGCTGCAAATGCAGTGAGAGATTACCAGAGGAAATTTCAAGAAATGAATgtaataattaaattacacgtttagtgcctcattagcctattgctacccttgtacttaaaattcaattcctgtgctaatcatagctatggccattaatcctttcattag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag
||| || ||||| ||  |||||||||||||  |||||||||| |||||||| || |||||||| || || || |||||||||||| |||| |||||||||||||   |  |  | | ||    |    |||   || | |     |   |  |||||   | |    || |||| |  |||||     || |   |       
GCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAATTTCAAGAGATGAATgtaactaaacacacttcataaagtctctaatttcttgt-cacaacaat-tgcctactgatgtag---gaataattcttgtttt----tgtctttcag------

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag
||| || ||||||||  | || || |||||  | ||||||||||||||||| || |||||||| || || || |||||||||||  |||| |||||||| ||||    | ||| |  || |||    |||    |   |  | ||     | ||  |  || |  ||  ||    | | |||| ||                 
GCTTACTCAGACTGTACGGGAACTGGAAGAGGCCGTTCTTGCTGGTGGTGCTGCTGCAAATGCCGTGAGGGATTACCAGCGGAAGTTTCAAGAGATGAACgtaa---gttaatac--atttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcag----------------

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaa--tacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag
||| | ||||| |||  | ||  |||||||| |||||||||||||||||||||||||||| || || ||||| |||||  ||||| | || || |||||||||   | |||        ||        ||   | |  ||  |||   | ||  |  ||  |   | |    |  | || | |       | |  | | |||||
GCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTGGTGGTGCAGCCGCAAACGCAGTGAGAGATTACCAAAGGAAATTCCAAGAAATGAATgtatatttcatatgcttctatagtacctcaataacttactgtttttcttgttag-tgttttggtctcgtactgatcgtaattgtggtgttttgtgttttccttag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 6
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctga----tgtccttggaaatgcattatgcgttttaggatatctacttgagcacca---tgactaatgcaa-gttttacaacgtttcctattcttag-----------------------
 || || || ||||| || ||||| |||||  ||||||| |||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||     | |  | |    |     | |||       |  | ||| ||| | | || ||  ||| |    || |  |||| | || ||  | | ||    | |  |                         
ACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTGGTGGTGCAGCTGCAAATGCTGTCAGAGATTACCAACGGAAAGTTCAAGAGATGAATgtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggct-tatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcag

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|67023844|gb|CO452593.1|CO452593
EST:     CAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAAT                         GAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCA
genomic: CAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatg ... ctattcttagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCA
EST: gi|24765000|gb|CA400161.1|CA400161
EST:     CAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAAT                         GAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCA
genomic: CAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatg ... ctattcttagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCA
EST: gi|6859889|gb|AW355883.1|AW355883
EST:     CAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAAT                         GAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCA
genomic: CAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatg ... ctattcttagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTGGTGGTGCAGCCGCAAATGCTGTCAGAGACTACCAGCGGAAAGTTCAGGAGATGAATgtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG