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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttgctcttcatattgctcagttatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA

Basic information

species Oryza sativa
transcript LOC_Os04g53240.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G419694_T05 (Zea mays), 3'ss of exon 3
gtaagcttgctcttcatattgctcagttatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA
|||||||||  |         |     |    ||||   ||| |  || ||  |||  || ||||| | ||| || | |  ||||| |||||||||||||||| ||||| || |||||||||||||||||||||||||||||
gtaagcttgtaccct------cctgcatgcactgttcgtttcttcatgattgctttcatccaatttatgaca-atgtga-ataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGATATTCCTGACATCGACAAGAAAAA

upper sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 4
gtaagcttgctcttcatattgctcagt-tatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA
|||||||||  |      ||  || || |    |||||| ||| |  |  ||  |||  || ||||| | ||   |    | ||||| |||||||||||||||| ||||| || ||||| |||||||||||||||||||||||
gtaagcttgtaccc----ttcttctgtatgcactgtttctttcttcat--ttgcttttatccaatttatgactagtt--gtataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA

upper sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
---gtaagcttgctcttcatattgctc---agttat--gttgtttccttcattgtggtttttt---tgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA
     || ||||    || ||   |     |||| |  |  || || |   || ||  | | |   || | |  ||  |||  | |||  ||  || ||||| ||||| ||||| |||||||||||||| || |||||||| |||||||| ||
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA

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:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|33670400|gb|CF298639.1|CF298639
EST:     CGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: CGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|86822106|gb|CI357784.1|CI357784
EST:     AAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: AAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|33655295|gb|CF277909.1|CF277909
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|38481968|gb|CF966032.1|CF966032
EST:     GTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|33688345|gb|CF316584.1|CF316584
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|86836082|gb|CI346147.1|CI346147
EST:     AGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: AGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|86418393|gb|CI032602.1|CI032602
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA
                                       atctaat  putative branch site (score: 3)
                          taatttgttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttgctcttcatattgctcagttatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA