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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatatttaaatacactagctgaatgcacatgctttgcgtcagaatttgaaaaagagaaccccaccatacactctaaagccccctaaacaacaaca...

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 4
ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaa-----cgatatttaaatacactagctgaatgcacatgctttgcgtcagaatttgaaaaagagaaccccaccatacactctaaagccccctaaacaacaaca
|| |||||  |  ||||| |||||||  |||||||||||||||||  |||||||||| ||| ||||||     | | ||||| || |  |   |   ||| ||  |||  | | |  || |    || |||     |  || || ||    |  | | ||   | ||  
ACGGATGACATACTGCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccctacatttatattctgtttttttttgcccactcttctctttattatgttttcaaaaga---ttaaaatgca-tcagtggttctcgaacttagaat-
















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|29623140|gb|CB628151.1|CB628151
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29623911|gb|CB628922.1|CB628922
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29661287|gb|CB657562.1|CB657562
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29630312|gb|CB635321.1|CB635321
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29624088|gb|CB629099.1|CB629099
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGCTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29681987|gb|CB678262.1|CB678262
EST:     GCACTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29672226|gb|CB668501.1|CB668501
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29679242|gb|CB675517.1|CB675517
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|88689613|gb|CI733189.1|CI733189
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29627005|gb|CB632016.1|CB632016
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29635022|gb|CB640031.1|CB640031
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAAGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29681845|gb|CB678120.1|CB678120
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29681724|gb|CB677999.1|CB677999
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29678406|gb|CB674681.1|CB674681
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29629756|gb|CB634765.1|CB634765
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29680593|gb|CB676868.1|CB676868
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29674493|gb|CB670768.1|CB670768
EST:     GCAGTTGTCAAAGGAGATCTAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29664072|gb|CB660347.1|CB660347
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29660244|gb|CB656519.1|CB656519
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29636080|gb|CB641089.1|CB641089
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTNTGAAGGGAAAACTGATGA
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGA
EST: gi|29639321|gb|CB644330.1|CB644330
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29629579|gb|CB634588.1|CB634588
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29617712|gb|CB622724.1|CB622724
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29665628|gb|CB661903.1|CB661903
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29629757|gb|CB634766.1|CB634766
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29678347|gb|CB674622.1|CB674622
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|29626366|gb|CB631377.1|CB631377
EST:     GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG
EST: gi|88367212|gb|CI563976.1|CI563976
EST:     GCAGTTGTCAAAGGAGATCAAGGGAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAA-CTGATGANTAAA-TCAAGACCATGGAAGTGGTGGAA
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGA-TAAAATCAAGACCATGGAAGTGGTGGAA
EST: gi|29656040|gb|CB652315.1|CB652315
EST:     GCAGTTGTCAAGGGAGATCGAGGAAAAAATGAAAGAAGTTGATACCTATG                         ATTTTGAAGGGAAAACTGATGATAAAATCAACACCATGGAAGTGGTGGAAG
genomic: GCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatat ... caacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATGgtaacgatatttaaatacactagctgaatgcacatgctttgcgtcagaatttgaaaaagagaaccccaccatacactctaaagccccctaaacaacaaca

- - - - - - - - - - - - AAGGAG
- - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - -  AGAAGT