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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacaacaatgaaatcctgctaatatttacagccttcaggtctatgcgtctatgatatcctaattgacatttgatattggaacctttgtcatatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTGAGCCGACCGATCAGGAGCTCAACGACATGATGAGGGAAGTTGATACAGA

Basic information

species Oryza sativa
transcript LOC_Os03g53200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G149923_T01 (Zea mays), 3'ss of exon 1
--acacaacaatgaaatcc---tgc-taatatt-tacagccttcaggtctatgcgtctatgatatcctaattgacatttgatattggaacctttgtcatatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTGAGCCGACCGATCAGGAGCTCAACGACATGATGAGGGAAGTTGATACAGA
     |     ||| | |    ||| ||   |  | ||  |    | | |     |||| ||     || ||||||  ||  | || || ||||| ||  |  ||||||||||||||| ||||||||||||| || || || ||||| || || || || |||| ||||||||||||||| || |||||||| || || ||||| ||
tggatctctgctgagacctgtgtgcgtagcgtagtgcaatcacaggcttttcttttctacgag----tagttgacaggtgg-aatgtaaactttgccaagt--gtagGATGCATCACCATGGAAGAGCTGGCCGCAGTCACCCGTTCCCTCGGTCTCGACCCGAGCGATCAGGAGCTCAATGATATGATGAGCGAGGTCGATACGGA
















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|88299931|gb|CI579992.1|CI579992
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTATTCGAAAAGAACGGCGATG                         GATGCATAACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|38472151|gb|CF956282.1|CF956282
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|29667976|gb|CB664251.1|CB664251
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88329564|gb|CI650016.1|CI650016
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88299406|gb|CI572358.1|CI572358
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88341641|gb|CI641393.1|CI641393
EST:     GATGGTGGCG-TCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCANCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCCTT
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGG-CCTT
EST: gi|88310980|gb|CI657893.1|CI657893
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88306356|gb|CI638139.1|CI638139
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88404677|gb|CI581113.1|CI581113
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGAAAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88827806|gb|CI778371.1|CI778371
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88407027|gb|CI581114.1|CI581114
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|58589123|gb|CF987431.1|CF987431
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|33656706|gb|CF279320.1|CF279320
EST:     GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: GATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
EST: gi|88404667|gb|CI581103.1|CI581103
EST:     ATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACCAAGAACGGGGATG                         GATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG
genomic: ATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGAC-AAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 44 (downstream exon)
Score: 16

TGTGACTGTGAAGGTGGCGGAGCCTGCATGGAAGGGCTGACGAGCGAGCAGATGGTGGCGTTCCAGGAGGCGTTCTTGCTCTTCGACAAGAACGGCGATGgttagtttca ... atatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTGAGCCGACCGATCAGGAGCTCAACGACATGATGAGGGAAGTTGATACAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtctatgatatcctaattgacatttgatattggaacctttgtcatatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTGAGCCGACCGATCAGGAGCTCAACGACATGATGAGGGAAGTTGATACAGA
                       atttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacaacaatgaaatcctgctaatatttacagccttcaggtctatgcgtctatgatatcctaattgacatttgatattggaacctttgtcatatatgtagGATGCATCACCTTGGAAGAGCTGGCTGCGGTGACTCGTTCTCTTGGCCTTGAGCCGACCGATCAGGAGCTCAACGACATGATGAGGGAAGTTGATACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- -caacaat
- - - - - - - -cctgcta
- - - - - - - - - - - - - - - - ccttcag
- - - - - - - - - - - - - - - - - - - - tctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatttg