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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaaaactctggtcattttggaatccaagttaatgttgaattatgtgttaagtctcacaactccccttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAATATAGTAGGCGTGTATTTGGTTCTGTTCTGAATGATGTTAGCCGTCGAGC

Basic information

species Zea mays
transcript GRMZM2G175676_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175676_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 4
gtgaggaaaactc--tggtcattttggaatccaagttaatgttgaattatgtgttaagtctcacaactccccttt--tgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAATATAGTAGGCGTGTATTTGGTTCTGTTCTGAATGATGTTAGCCGTCGAGC---
|||||  |   ||  |  || |||   |||  |||  | |||    || |   |||| ||| |||| |||| |||  || |||||||   | |||||| || ||| ||||||| ||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||||||  |   
gtgagagagtttccttattcctttcaaaatataagacactgtatggtttttaattaaatcttacaattcccttttcttgtccagCAC---CAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATAGTAGACGCGTATTTGGTTCTGTTCTGAATGACGTTAGCCGTCGTACTGA
















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|60339325|gb|DN206298.1|DN206298
EST:     GTATCCCACCAAATCATTCATACGACACGCACACTCAAG                         CACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
genomic: GTATCCCACCAAATCATTCATACGACACGCACACTCAAGgtgaggaaaa ... ttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
EST: gi|60355014|gb|DN221987.1|DN221987
EST:     TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAG                         CACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
genomic: TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAGgtgaggaaaa ... ttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
EST: gi|60345015|gb|DN211988.1|DN211988
EST:     TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAG                         CACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
genomic: TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAGgtgaggaaaa ... ttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
EST: gi|31558437|gb|CD527649.1|CD527649
EST:     TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAG                         CACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
genomic: TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAGgtgaggaaaa ... ttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
EST: gi|161585690|gb|EY953332.1|EY953332
EST:     CGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAG                         CACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACGTATGAAT
genomic: CGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAGgtgaggaaaa ... ttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
EST: gi|71445511|gb|DR826561.1|DR826561
EST:     TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAG                         CACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT
genomic: TGCCGGGTATGGTATCCCACCAAATCATTCATACGACACGCACACTCAAGgtgaggaaaa ... ttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccaagttaatgttgaattatgtgttaagtctcacaactccccttttgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAATATAGTAGGCGTGTATTTGGTTCTGTTCTGAATGATGTTAGCCGTCGAGC
                              gtctcac  putative branch site (score: 3)
                                       ctccccttttgacc  putative PPT
        ttaatgttgaattat  TA-rich tract