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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_Os01g01307.2
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|5004937|gb|AU070175.1|AU070175
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|88975507|gb|CI021589.1|CI021589
EST:     AAGAAGTTTGAATGGGCTAAG
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|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|55431326|gb|CV728677.1|CV728677
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86415683|gb|CI029694.1|CI029694
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|88267065|gb|CI379000.1|CI379000
EST:     AAGAATTTTTAATGGGCTAAG
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|88228632|gb|CI228112.1|CI228112
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86415979|gb|CI029990.1|CI029990
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|87032410|gb|CI264191.1|CI264191
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|86839596|gb|CI339491.1|CI339491
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86413465|gb|CI067870.1|CI067870
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|86416814|gb|CI030825.1|CI030825
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|33809715|gb|CF330747.1|CF330747
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctagtgcatctatggtagaagaaattactgagaaattatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG
                                            tccattt  CT-rich tract
                        aagaaatta  TA-rich tract