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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgcactgatttgactaatgttatcgcgacactatatcag

Basic information

species Zea mays
transcript GRMZM2G174170_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174170_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g20340.1 (Oryza sativa), 5'ss of exon 3
AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgca-ctgatttgactaatgttatcgcgacactat-atcag
| || || || || || |||||||| || ||||||||||||||||| |||||||||||||||||| | || |  || ||  |  ||           |  | | | |||| | |||||||| |  || |  |||||| ||  |  |||| || | |||
AACAGTGCGAAAGAGATAAAGCACGTGTTCTAGTCCATTGCATGTCAGGGAAAAGTAGgtgtgtacg-tatacttgaattctcgtt-----------ggcagattttttcatgtttctgcatccaatatatctaatgctactgaaacacaattaccag

upper sequence: GRMZM2G174170_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G04550.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgcactgatttgactaa--tgttatcgcgacactatatcag-----------------
| |||||||||| ||| || ||||| || || || |||||||||||||||||||||||||| |||   |    ||     |  | |||||               |||||||||   | |  | | ||   ||   |  ||  | || |   | |  |                 
ACCAATGTGAGAAGGACAAGGCACGTGTTCTTGTGCATTGCATGTCTGGGAAAAGTAGgtgagtacatttatcattctcttactctcatcctaaacttgcggctgctttcttatgattaccattaattatttagactaatagagtgatatgttttgtgtttcgattacatgacag
















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|78111707|gb|DV530104.1|DV530104
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|78107085|gb|DV525503.1|DV525503
EST:     AAG-GGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: -AGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|211350508|gb|FL033065.1|FL033065
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGTAGAT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTT-GTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGAT
EST: gi|71301897|gb|DR787018.1|DR787018
EST:     GAGAGGGAGAAAGCACGAGTCTTAGTCCATTGCATGCCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|91875180|gb|EB405137.1|EB405137
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|149112681|gb|EE295513.2|EE295513
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|71314755|gb|DR794000.1|DR794000
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|211350512|gb|FL033069.1|FL033069
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA--A-                         -TCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|78107086|gb|DV525504.1|DV525504
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|91055824|gb|EB166242.1|EB166242
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|71299488|gb|DR785755.1|DR785755
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|84969786|gb|DW468209.1|DW468209
EST:     GCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|78118997|gb|DV537381.1|DV537381
EST:     AGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: AGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|211350511|gb|FL033068.1|FL033068
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAA--A-                         -TCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|76925731|gb|DV170569.1|DV170569
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGTAATAGCCTTCTTGATGAAGTCGAGAGGTTGGAGATT
EST: gi|211352915|gb|FL033076.1|FL033076
EST:     GAGAGGGAGAAAGCACGAGTCCTAGTCCATGGCATGTCTGGGAAAAGTAG                         ATCGGCAGCTTTTGT
genomic: GAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatgg ... actatatcagATCGGCAGCTTTTGT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAATGTGAGAGGGAGAAAGCACGAGTCCTAGTCCATTGCATGTCTGGGAAAAGTAGgtgtgtatggtacatatgtatattttttcatctgggggagctataatctttcttatttctgcactgatttgactaatgttatcgcgacactatatcag

- - - - GAGAGG
- - - - - -  GGAGAA