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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttctatatatcatattgcacagtattgccaatttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g38960.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086904_T01 (Zea mays), 3'ss of exon 3
gtatgtttctatatatcatattgcacagtattgccaatttgatg-gctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG
                    ||  | | | |||    ||  |   |  || |   || | | ||    |||||         ||  ||||  ||||||||||||||||| ||||||||||||||||| |||||||| |||||||||
-------------------gtta-ataattttgagtgttgaacatgtaaaaaacctatcttccaac-ctaatactaaccttagtctttttgcagCATGAATGCTCCAGTCATGGTTGAGCTTGAGGGTGAAACTGACCCTCTTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G013600_T01 (Zea mays), 3'ss of exon 3
gtatgtttctatatatcatattgcacagtattgccaatttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG
       |  |||  | ||| |    ||| |||   || | |  ||||     || | |   | || ||||    |||  |  | ||||  ||||||||||||||||| |||||||||||||||||||||||||| |||||||||
------gttaatagttaatact----agtgttgagcatgtaaaagctatc---ttgcaacctaatactaat----ctt--tagtcttttgcagCATGAATGCTCCAGTCATGGTTGAGCTTGAGGGAGAAACTGACCCTCTTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G013600_T02 (Zea mays), 3'ss of exon 3
gtatgt---ttctatatatcatattgcacagtattgccaat-ttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG
|||         |  | || |  ||      || | | | | ||||      | |   || | | ||    |||||    |   |  | ||||  ||||||||||||||||| |||||||||||||||||||||||||| |||||||||
gtacacgagccttgcagataaggttaatagttaatactagtgttgagcatgtaaaagctatcttgcaac-ctaatactaatctttagtcttttgcagCATGAATGCTCCAGTCATGGTTGAGCTTGAGGGAGAAACTGACCCTCTTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G51940.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtttctatatatcatattgcacagtattgccaatttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG
||||| ||||   |   |    | ||| | ||   ||| | |       | |   |   |  ||| |||||     ||  ||   |  || |||||||||||||| || ||||||||||| ||||| || |||||||| ||||||
gtatggttct---tgctactgagaacaatctttttaatgttaaattggcttgaaaagtttg-agtcttaatgttgttttttggc-tgatacagCATGAATGCTCCTGTCATGGTTGAGCTAGAGGGTGAGACTGATCCACTTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G04630.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtttctatatatcatattgcacagtattgccaatttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG
||  | | ||    |  || ||     |  |  ||  || | |||||   |   |   || |  | |     ||  ||| ||   |  || |||||||||||||| |||||||||||| | ||||| || |||||||| ||||||
gtcagctactgagaacaatctt-tgttgattaaccgtttagttggctcggaaagtttgattctatgt-----actgttgttggc-tgatacagCATGAATGCTCCTGTTATGGTTGAGTTGGAGGGTGAGACTGATCCACTTGAG

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|88215899|gb|CI215748.1|CI215748
EST:     ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCCCTTGA
genomic: ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|86506229|gb|CI148862.1|CI148862
EST:     TCCTGGGTAAACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGCTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: TCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|88517263|gb|CI444917.1|CI444917
EST:     GCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: GCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|38481397|gb|CF965486.1|CF965486
EST:     ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|86416666|gb|CI030677.1|CI030677
EST:     CCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: CCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|86536627|gb|CI176833.1|CI176833
EST:     ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|88216290|gb|CI216139.1|CI216139
EST:     CGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: CGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|86507172|gb|CI149805.1|CI149805
EST:     CGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: CGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|88907433|gb|CI090227.1|CI090227
EST:     ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|88289429|gb|CI555791.1|CI555791
EST:     CACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: CACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|38468521|gb|CF952652.1|CF952652
EST:     ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: ACAAAGTATGAGCGTGCCCGCATCCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
EST: gi|86911562|gb|CI296648.1|CI296648
EST:     CCTGGGTACACGTGCATTACAGATAAG                         CATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA
genomic: CCTGGGTACACGTGCATTACAGATAAGgtatgtttct ... tgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG
                             taataac  putative branch site (score: 1)
                                            ttgtttt  putative PPT
                    atacagtattaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttctatatatcatattgcacagtattgccaatttgatggctaatagtttaccatacagtattaataacccttgctgttgttttatagCATGAATGCTCCAGTTATGGTTGAGCTTGAGGGAGAAACTGATCCTCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA