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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccaaaataaaccctacataaatattgtgaaatgcttagaatttcaacctggctattattttgcttcagtaatatggttttcgtttttaagatggcattttctaataggaagggaatgataacttcatagcttccattgttataaatatatctgaccaccaatatcttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT

Basic information

species Oryza sativa
transcript LOC_Os03g16010.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G479243_T01 (Zea mays), 3'ss of exon 3
gtaagaccaaaa---taaaccctacataaa-------tattgtgaaatgcttagaatttcaacctggctatt-----attttgcttcagtaatatggttttcgtttttaagatggcattt-tctaataggaagggaatgataacttcatagcttccattgttataaatatatctgaccaccaatatcttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT
|||||| ||||     |  |  ||    ||       | ||||||  ||||||  |||| |  || | |||      |||||||  ||||||| || ||||  ||  |  ||| | |||| |||||||  | | |||||| |  |   || |||| ||   | ||   |||  |  |   |    || ||| || |||||||||||||| ||||  ||||||||||||||||| |||||||||||||||||||||||||||||| |  |
gtaagaacaaagaaccattctttaagctaacttggtttgttgtgatctgcttaatatttta-tctagatatctacagattttgcaacagtaatttgttttt--ttaatgggatagaatttctctaatatta-gagaatgaaatttcagtatcttctatcaatgtag-cataaatatctgacttactcctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTT

upper sequence: LOC_Os03g16010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G886952_T01 (Zea mays), 3'ss of exon 3
gtaagaccaaaa---taaaccctacataaa-------tattgtgaaatgcttagaatttcaacctggctattattttgcttcagtaatatggttttcgtttttaagatggcattt-tctaataggaagggaatgataacttcatagcttc---cattgttataaatatatctgaccaccaatatcttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT
|||||| ||||     |  |  ||    ||       | |||| |  ||||||  |||  |  || |||||   |    ||  | || |         ||| |  ||| | |||| |||||||  | | |||||| |  |   || ||||   || |||   | | |||||||||   |    || ||| || |||||||||||||| ||||  ||||||||||||||||| || |||||||||| |||||||||||||||| |  |
gtaagaacaaagaaccattctttaagctaacttggtttgttgttacttgcttaatattgta-tctagctat--ctacagttttgcaacactaacaatttttatgggatagaatttctctaatacta-gagaatgaaatttcagtatcttctagcaatgtagcataaatatctgacttac----tcctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT
















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|58663052|gb|CK051738.1|CK051738
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58666565|gb|CK055251.1|CK055251
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|29629426|gb|CB634435.1|CB634435
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58669498|gb|CK058184.1|CK058184
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58652532|gb|CK041212.1|CK041212
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGT
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGT
EST: gi|58607723|gb|CK035756.1|CK035756
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCTTATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58672896|gb|CK061582.1|CK061582
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|29629423|gb|CB634432.1|CB634432
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58653189|gb|CK041869.1|CK041869
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58669348|gb|CK058034.1|CK058034
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|58655196|gb|CK043876.1|CK043876
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
EST: gi|33796848|gb|CF324289.1|CF324289
EST:     AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCT                         GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG
genomic: AATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAG

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: 61 (upstream exon), 72 (downstream exon)
Score: 27

CTTCTGATGGGATATTTCTCAACTGGCGTGAACAAGATGTGGATCCTTGCAATTGGAAGGGTGTTGGATGTGACTCTCACACCAAGAGAGTAGTTTGTCTgtaagaccaa ... ttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcatagcttccattgttataaatatatctgaccaccaatatcttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT
                                           tcttttgttt  CT-rich tract
              attgttataaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccaaaataaaccctacataaatattgtgaaatgcttagaatttcaacctggctattattttgcttcagtaatatggttttcgtttttaagatggcattttctaataggaagggaatgataacttcatagcttccattgttataaatatatctgaccaccaatatcttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT