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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttactctttgttttattctacaaggagcaacttttctagtgcatctatggtagaagaaattactgagaaattatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g01307.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G376727_T04 (Zea mays), 3'ss of exon 5
--------------------------gtaaatttactctttgttttattctacaag------gagcaacttttctagtgcatctatggtagaagaaattactgagaaa-----ttatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG---
                          || |||||  || ||||     |  | |||        | |  |||     | ||| |    | ||       |   | |||     |||||||| ||||||||||||||||||| || ||||| || ||||| |||||    || |||||| ||||||||||||| ||||| |||||||| ||    ||| |  ||||||   
gtatttctgtttttccgtctacttttgtcaattt--tccttgtccatctaaataagctgctcaggtagatttaagcattcatttgacctggacactgacaaaaaaaaaaattgttatccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAG---AGCAGCTCAAAAGGAA

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G067476_T03 (Zea mays), 3'ss of exon 3
----gtaaatttactc--tttgttttattcta--caaggagcaacttttctagtgcatctatggtagaagaaattactgagaa--attatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG---
    || ||||| |    ||  | | | |  |        |||  ||||    | ||| |  | | ||    |  |   | ||   |||||||| ||||||||||||||  ||| |||||||| || ||||| |||||    || |||||| ||||||||||||| || || |||||||| ||    ||| |  |||| |   
tctggtcaatttccctagttcatctaaataaaattttcaggcagattttaccattcatttgagctggacactaacaaaaaaaattgttatccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGGACTGTTTATCTACCTTGTCGCGAGCCCGTCGAAG---AGCAGCTCAAAGGCAA

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G376727_T03 (Zea mays), 3'ss of exon 4
-gtaaatttactctttgttttattctacaag------gagcaacttttctagtgcatctatggtagaagaaattactgagaaa-----ttatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG---
 || |||||  || ||||     |  | |||        | |  |||     | ||| |    | ||       |   | |||     |||||||| ||||||||||||||||||| || ||||| || ||||| |||||    || |||||| ||||||||||||| ||||| |||||||| ||    ||| |  ||||||   
tgtcaattt--tccttgtccatctaaataagctgctcaggtagatttaagcattcatttgacctggacactgacaaaaaaaaaaattgttatccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAG---AGCAGCTCAAAAGGAA

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G067476_T01 (Zea mays), 3'ss of exon 5
--------------------------gtaaatttactc--tttgttttattcta--caaggagcaacttttctagtgcatctatggtagaagaaattactgagaa--attatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG---
                          || ||||| |    ||  | | | |  |        |||  ||||    | ||| |  | | ||    |  |   | ||   |||||||| ||||||||||||||  ||| |||||||| || ||||| |||||    || |||||| ||||||||||||| || || |||||||| ||    ||| |  |||| |   
gtatttttctctttccctctactctggtcaatttccctagttcatctaaataaaattttcaggcagattttaccattcatttgagctggacactaacaaaaaaaattgttatccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGGACTGTTTATCTACCTTGTCGCGAGCCCGTCGAAG---AGCAGCTCAAAGGCAA

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|88249475|gb|CI249324.1|CI249324
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88908088|gb|CI090684.1|CI090684
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88976399|gb|CI024616.1|CI024616
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|89185624|gb|CI264305.1|CI264305
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86506952|gb|CI149585.1|CI149585
EST:     AAGAAGTTTGAATGGACTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|33693728|gb|CF321967.1|CF321967
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|55431192|gb|CV728603.1|CV728603
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|55441563|gb|CV734105.1|CV734105
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|5002911|gb|AU068020.1|AU068020
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|87010511|gb|CI283586.1|CI283586
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86532074|gb|CI172280.1|CI172280
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15848576|gb|BI796852.1|BI796852
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86530842|gb|CI171048.1|CI171048
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88907999|gb|CI090595.1|CI090595
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15852886|gb|BI805682.1|BI805682
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86522288|gb|CI162494.1|CI162494
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|87032410|gb|CI264191.1|CI264191
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|55431326|gb|CV728677.1|CV728677
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86415683|gb|CI029694.1|CI029694
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|25807463|gb|CA763424.1|CA763424
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86416814|gb|CI030825.1|CI030825
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88267065|gb|CI379000.1|CI379000
EST:     AAGAATTTTTAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88975507|gb|CI021589.1|CI021589
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|87027081|gb|CI261528.1|CI261528
EST:     AAGAAGTTTGAATGGGCTGAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|55431655|gb|CV728843.1|CV728843
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|33816593|gb|CF334128.1|CF334128
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|33660042|gb|CF291009.1|CF291009
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86530806|gb|CI171012.1|CI171012
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88320313|gb|CI520857.1|CI520857
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|58594778|gb|CF993086.1|CF993086
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88228632|gb|CI228112.1|CI228112
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86415979|gb|CI029990.1|CI029990
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88837885|gb|CI371463.1|CI371463
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|12405401|gb|AU167002.1|AU167002
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|427829|gb|D23969.1|D23969
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|5004937|gb|AU070175.1|AU070175
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86839596|gb|CI339491.1|CI339491
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86413465|gb|CI067870.1|CI067870
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|33809715|gb|CF330747.1|CF330747
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG

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), 70 (downstream exon)
Score: 70

GCTAAGgtaaatttac ... ccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctagtgcatctatggtagaagaaattactgagaaattatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG
                                            tccattt  CT-rich tract
                        aagaaatta  TA-rich tract