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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaatctgttacacttacacacttttttaaaacttcagctcttttttttttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG

Basic information

species Oryza sativa
transcript LOC_Os01g01307.2
intron # 3
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 3
lower sequence: GRMZM2G067476_T02 (Zea mays), 3'ss of exon 3
gtttaatctgttacacttacacacttttttaaaacttcagctcttttttttttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG----
 |   |  ||  |   || |  ||| |    | | || ||   | ||| || ||  |   ||       |  |  || || |  |   |||||  ||| |    ||| |||||||||| || ||||| |||||| |  |||| ||| |||| |||||||| |||||||| |||||||||||||||    
-tccgacttgaaaacattgc-tactgtac--ataatttagtagtgtttcttgtattgtccaac------ccacggtgttt-cgctaaatcaatgctttgt--acatgttgaagGAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGGGTAA

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G376727_T03 (Zea mays), 3'ss of exon 3
-------------------------------gtttaatctgttacacttacacacttttttaaaacttcagc-tcttttttttttaaagaaaaatgctgttctgct-atgct-tgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG----
                                |  |   | |||   || |  |  || |  |   |  |   || | || ||||  | |    |  || |  ||  ||| | |  | ||        | |||| | | || | ||||||||||| ||||| |||||| |  |||| ||| |||| |||||||| | ||| || |||||||||||||||    
gtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcctcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaagGAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAA

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G067476_T01 (Zea mays), 3'ss of exon 3
gtttaatctgttacacttacacacttttttaaaacttcagctcttttttttttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG
 |   |  ||  |   || |  ||| |    | | || ||   | ||| || ||  |   ||       |  |  || || |  |   |||||  ||| |    ||| |||||||||| || ||||| |||||| |  |||| ||| |||| |||||||| |||||||| |||||||||||||||
-tccgacttgaaaacattgc-tactgtac--ataatttagtagtgtttcttgtattgtccaac------ccacggtgttt-cgctaaatcaatgctttgt--acatgttgaagGAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGG

upper sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 3
-------------------------------gtttaatctgttacacttacacacttttttaaaacttcagc-tcttttttttttaaagaaaaatgctgttctgct-atgct-tgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG
                                |  |   | |||   || |  |  || |  |   |  |   || | || ||||  | |    |  || |  ||  ||| | |  | ||        | |||| | | || | ||||||||||| ||||| |||||| |  |||| ||| |||| |||||||| | ||| || |||||||||||||||
gtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcctcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaagGAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG

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:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88908088|gb|CI090684.1|CI090684
EST:     GTTCACCTGCGGTTATNACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88976399|gb|CI024616.1|CI024616
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|5004937|gb|AU070175.1|AU070175
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86506952|gb|CI149585.1|CI149585
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88975507|gb|CI021589.1|CI021589
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|55431192|gb|CV728603.1|CV728603
EST:     GGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|55441563|gb|CV734105.1|CV734105
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|87010511|gb|CI283586.1|CI283586
EST:     CAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: CAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86532074|gb|CI172280.1|CI172280
EST:     AGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTACACTTGATGTTCTTGCTGAGAGGCCT
genomic: AGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86530842|gb|CI171048.1|CI171048
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88907999|gb|CI090595.1|CI090595
EST:     CACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: CACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|15852886|gb|BI805682.1|BI805682
EST:     GTTCACCT-CGGTTA-TACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GA-GCCTATTCAACCCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAA-CCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
EST: gi|86415683|gb|CI029694.1|CI029694
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|87027081|gb|CI261528.1|CI261528
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAGCCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|55431655|gb|CV728843.1|CV728843
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|33660042|gb|CF291009.1|CF291009
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAA-CCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCC
EST: gi|88228632|gb|CI228112.1|CI228112
EST:     ACCTGCGATTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: ACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86415979|gb|CI029990.1|CI029990
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|87032410|gb|CI264191.1|CI264191
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|88837885|gb|CI371463.1|CI371463
EST:     CACAAA-GCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGA-GCCT
genomic: CACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|427829|gb|D23969.1|D23969
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86413465|gb|CI067870.1|CI067870
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
EST: gi|86416814|gb|CI030825.1|CI030825
EST:     GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAG                         GAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT
genomic: GTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCTGCGCTTCAGgtttaatctg ... tatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG
                                  ttttttttttgtat  CT-rich tract
                              tcaattttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatctgttacacttacacacttttttaaaacttcagctcttttttttttaaagaaaaatgctgttctgctatgcttgcaattgctcaattttttttttgtatggtgaagGAGGCCTATTCAACCCCCATCCTTGCACTTGATGTTCTTGCTGAGAGGCCTCCAGAAAAGAAGTTTGAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT