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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattgatgtgggatgatcctattttcttatctattgtcattgatcccaaataaaataataatcttgtggttactgtagactgtagagcatcttgtttcaatactgcagctattatttgtggaattgacaatgtaattcctttttctttccccctcacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCCTACTTTCTGGGATTTCTTG

Basic information

species Zea mays
transcript GRMZM5G871861_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871861_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g10340.1 (Oryza sativa), 3'ss of exon 3
gtttattgatgtgggatgatcctattttcttatctattg--tcattgatcccaaataaaataataatcttgtggtta------ctgtagactgtag----agcatcttgtttcaatactgcagctattat------ttgtggaattgacaatgtaa-------------ttccttt--ttctttccccctcacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCCTACTTTCTGGGATTTCTTG
||  ||||||   | ||||| ||    ||| |||   ||  |||||||| | |||| |   | |    ||  ||||          |||  || |     ||        |  ||||||  |   ||| |      || |  |||| ||| || |              |||||||  || ||      |     ||||||| |||||||||||||||||||||||||| ||||  |||||| |  |  ||||||| ||||||||| |||
gtgcattgatacagaatgattctgacctctcatcccatgattcattgatgcgaaatgatcaacttgatttccggtttgatatctaatagcatgcaaaagtagggggaaagtggaatactagaatcattgtagtttattctacaattaacattgcagagtgttgtaaatcttcctttaatttttcttattttgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCCTACTTACTGGGATTTGTTG
















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|211149058|gb|FK958475.1|FK958475
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTA
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTA
EST: gi|22546278|gb|BU098589.1|BU098589
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGTTGGCTGGCCTTTGCC
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
EST: gi|149004383|gb|EE039059.2|EE039059
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
EST: gi|13557642|gb|BG548998.1|BG548998
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
EST: gi|78113561|gb|DV531952.1|DV531952
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
EST: gi|71449411|gb|DR830461.1|DR830461
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
EST: gi|149001459|gb|EE038760.2|EE038760
EST:     AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG                         GGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC
genomic: AAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAGgtttattgat ... cacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatttgtggaattgacaatgtaattcctttttctttccccctcacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCCTACTTTCTGGGATTTCTTG
                                         ccctcac  putative branch site (score: 3)
                          ttcctttttctttccc  CT-rich tract
                   aatgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattgatgtgggatgatcctattttcttatctattgtcattgatcccaaataaaataataatcttgtggttactgtagactgtagagcatcttgtttcaatactgcagctattatttgtggaattgacaatgtaattcctttttctttccccctcacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCCTACTTTCTGGGATTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG