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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatttaacagcaacaatggacttgaattattcctgttcatttttcttgccatgaaattgtttcatccaagattctgttttctgtaataaacaactgccttttccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG

Basic information

species Oryza sativa
transcript LOC_Os01g60660.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G166345_T04 (Zea mays), 3'ss of exon 7
gtgagtatttaacagcaacaatggacttgaattattcctgttcatttttcttgccatg-aaattgtttcatccaagattctgttttctgtaataaacaactgcct----tttccttca--cagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG-------------------------------
||||||| ||| | |||| || | |||  |||| ||  ||  ||||||   |  |||  ||  ||||| | | | | | |||| || ||  || |||| ||| ||    ||| ||||   ||||||||||||||||| || |||||||||||||||||||| ||||||||||| ||||||||||| ||||||                               
gtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTGGTATGTCCTATCTATTATAATTGCATTTGTG

upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 7
gtgagtatttaacagcaacaatggacttgaattattcctgttcatttttcttgccatg-aaattgtttcatccaagattctgttttctgtaataaacaactgcct----tttccttca--cagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG
||||||| ||| | |||| || | |||  |||| ||  ||  ||||||   |  |||  ||  ||||| | | | | | |||| || ||  || |||| ||| ||    ||| ||||   ||||||||||||||||| || |||||||||||||||||||| ||||||||||| ||||||||||| ||||||
gtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG
















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|89189180|gb|CI048719.1|CI048719
EST:     TCAGCCCAGAGGAACTTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGA
genomic: TCAGCCCAGAGGAAC-TTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGA
EST: gi|86594926|gb|CI258180.1|CI258180
EST:     AGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: AGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|58688789|gb|CK077476.1|CK077476
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|86418870|gb|CI053671.1|CI053671
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|86492758|gb|CI135391.1|CI135391
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|86434980|gb|CI106213.1|CI106213
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|29672822|gb|CB669097.1|CB669097
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|86823873|gb|CI258854.1|CI258854
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|29642064|gb|CB647071.1|CB647071
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|29642108|gb|CB647115.1|CB647115
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
EST: gi|58694983|gb|CK083670.1|CK083670
EST:     ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT                         AATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC
genomic: ATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtattt ... tccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcatccaagattctgttttctgtaataaacaactgccttttccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG
                                     ctgccttttccttcac  CT-rich tract
                    ttttctgtaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatttaacagcaacaatggacttgaattattcctgttcatttttcttgccatgaaattgtttcatccaagattctgttttctgtaataaacaactgccttttccttcacagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC