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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA

Basic information

species Zea mays
transcript GRMZM2G047223_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 4
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattc--tattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
|||||| || |    | ||||   ||||   | ||| |   || ||| | || ||||||    | |  ||| || ||| |||  |||||||||||||||||||||||||  |||| ||||||||||||||||| || |||||||| ||||||||||| || ||||| ||||||||||| ||||| ||||
gtttgtgttaaaactgctgactagttttaggatataaacttat-tctgttgagtaatatgtgttctcttttgcataat-catgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
-gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
  |||  |  |    |  | |||| | | | |   |   ||  | | ||    ||||||||  ||  |||  | |        | ||||| ||||| |||||||| || ||  |||||||||||||||| |||||||||||||| ||||| || || || |||||||| ||||| || ||||| ||||
gttttactcaggaacccatcacctttctgtgcttgttacaaagtatttc----ataatattg-atcattttaaaa-------ctacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
-gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
  |||  |  |    |  | ||||   | | |   |   ||  | | ||    ||||||||  |   |||  | || ||      ||||| |||||||||||||| |||||  ||||||||||||||||||||||||||||||| ||||| || || || |||||||| ||||| || ||||| ||||
gttttactcaggaccccatcaccttgctgtgcttgttacaaagtatttc----ataatattg-accattt-taaaactc------cagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcat-tttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
|| | |  |        |  |||  |||  ||  |       |   | | | ||   |  |||   || |      | || | ||||||| ||||| ||| |||| ||  || ||||||| |||||||| || || ||||| |||||||||||||| || || || || |||||||| ||||| ||||
gtctatcctctagatatttcccttgtttcccattttt---ctttcttttagtatggga--ctaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
|| | |   ||| ||  |  | |  || ||        |||||    ||  ||| |      | |  |   || |   ||  ||||||||||||| ||  |||| ||  || |||||||||||||||| || || |||||||||||||||||||| || || || || |||||||||||  | ||||
gtatttccagagatcttttcctttattcttatttgcccaagatggtact--aattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
gtttg----ttttgagttcggtgacctattttttca--gatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
|||||    |  ||  |    | ||   | | || |  | | | | |||       |||| | |||  ||||     |   ||     |||||||||||||||||||||||||  | |||||||||||||||||||| || ||||||||||||||  | || || || || || |||||||| ||||| ||||
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatact----gaatgacattggattg---gtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27331 (Selaginella moellendorffii), 3'ss of exon 3
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
             |  | |    | ||| |||  |    | |      ||  |   |  || ||  |  |             |||||||||||| |||||||| ||  |||||||| | || ||| ||||||||||||| || |||||  | || ||| || | ||||| || || ||||| ||||
------------gtaagagcgacactttctcacgtttggaaacaatgttgttaagctcctcgatcatccatga--------ccgcagGGAATGGGTTTTTTAGCAGGCTTGCTGCTTTTGTACATGTGTGAGGAGGATGCGTTTTGGTTGCTTGTGGCGCTGTTGAAGGGCGCAGTTCATGCGCCAA

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|78113905|gb|DV532294.1|DV532294
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGTTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|89247292|gb|DY619078.1|DY619078
EST:     ACATTTTGAAAGCATATTCTGTTTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGTTGCTGC-TCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|211004390|gb|FL335892.1|FL335892
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTT-AGCT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCT
EST: gi|61118400|gb|DN559361.1|DN559361
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|78118514|gb|DV536898.1|DV536898
EST:     TTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: TTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|89758012|gb|DY687355.1|DY687355
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGTTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|91874336|gb|EB404293.1|EB404293
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|78117555|gb|DV535942.1|DV535942
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|71771758|gb|DR969695.1|DR969695
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGGTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
EST: gi|78118515|gb|DV536899.1|DV536899
EST:     ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAG                         GGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT
genomic: ACATTTTGAAAGCATATTCTGTCTATGACAGGGATGTTGGATATGTGCAGgtttgttttg ... cattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
                                           ttcatttt  CT-rich tract
                   aataatattctattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT