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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccgtatcatccttagtagcttatgattttctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os04g53240.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 5
gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccgta-tcatccttagtagcttatgattttc-taa---tatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG
   | ||| |  | |   |     ||  |   |||  | | |     |||   |       ||| || | | |  ||     || ||||| || |||   |  |||||||| ||||||||||||||||| ||||| || || || ||||||||| ||||| | |||||||||||| |||||||||| ||||||||||||||||||
---caaaaatact-tcattaaagcaccattgcacacatcaaagtgt-tatgtgttgtgtcaaccatagtaagcaataagctgttctgattgtcataactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG

upper sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G419694_T05 (Zea mays), 3'ss of exon 4
--gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccgtatcatccttagtagcttatgattttctaatat--agGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG
        || |  |  |||  | || | ||| | ||    |||||||  | | |     |       |   | || | |  || |||    || | | |  |||||||| |||||||| |||||||| || ||||| || || ||||||||| ||||| | |||||||||||| ||||||| || |||||||| |||||||| 
acaaaaagaaatgctactgcattaaagcattattgcac---acatcaaa-agcgagttgcagccgtaaactgttctgattttctgatggccatcaactttgcagGTACCTCGTCCCTGCAGATCTTACAGTCGGGCAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAGGCTATCTTCATATTTGTGAAA

upper sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccg--tatcatccttagtagcttatgattttctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG
  | | |  ||||     ||    | | |  || ||| || ||      | |    || ||| |   ||| ||||| |||  ||  |   |    |||  || || ||||| ||||||||||| || |||||||||||||| |||||  | |||||| |||||||||| ||| ||||||| || || ||||| ||||| |||
--tagtatgttttcacattcgattattgtcttatatggtaaattcctgtttagctgattttatcaaatattatcctgagttcctacttcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG

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|33655349|gb|CF277963.1|CF277963
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|14981112|gb|BI305803.1|BI305803
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|33670400|gb|CF298639.1|CF298639
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTTTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|89179617|gb|CI391950.1|CI391950
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|86822106|gb|CI357784.1|CI357784
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|86418393|gb|CI032602.1|CI032602
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|88477680|gb|CI414951.1|CI414951
EST:     GACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: GACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|33655295|gb|CF277909.1|CF277909
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCCGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|38481968|gb|CF966032.1|CF966032
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|33688345|gb|CF316584.1|CF316584
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|86836082|gb|CI346147.1|CI346147
EST:     ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: ATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
EST: gi|88272085|gb|CI388138.1|CI388138
EST:     AAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG
genomic: AAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttcc ... tctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatcaatcaatattaccgtatcatccttagtagcttatgattttctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG
                                            ttctaat  putative branch site (score: 2)
                                          ttttct  CT-rich tract
                                    ttatgattttctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccgtatcatccttagtagcttatgattttctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA