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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgacaatcttcattcacctgtgatttgtgttgtcacgatttgcattactgatttcattctgtttctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTTGATGAGGCAGGGGCTTGGAAAAGCAAGCTTCAACCAGAATCCAGGCAAC

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 2
gtttgacaatcttcattcacctgtgatttgtgttgtc-acgatttgcattactgatttcattctgtttctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTTGATGAGGCAGGGGCTTGGAAAAGCAAGCTTCAACCAGAATCCAGGCAAC
|||||||  |||   |||   ||||| | |||||  |          ||||||||  | | ||  |||||||   |||||||||||||||| || ||||||||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||  | ||||| ||| | |
gtttgac--tctatgttc---tgtgact-gtgttacccgtagaacatattactgacataactccttttcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGGCTGAATCAAGGGAGC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 9
gtttgacaatcttcattcacctgtga-tttgtgttgtcacgatttgcattactgatttcattctgtttctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTTGATGAGGCAGGGGCTTGGAAAAGCAAGCTTCAACCAGAATCCAGGCAAC
||||| || || | ||    || ||| ||||||||||||   | |  ||||||||  ||| ||| |||||||   |||||||||||||||| || |||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || ||||| ||| | |
gtttggcactccttatgt-tctatgactttgtgttgtca--gtctatattactgacatcactct-tttctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGCCTGAATCAAGGGAGC
















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|88504577|gb|CI432083.1|CI432083
EST:     ACTATGGTNTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|29689204|gb|CB685479.1|CB685479
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|157650204|gb|EX449838.1|EX449838
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|88365473|gb|CI680112.1|CI680112
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|88369740|gb|CI680411.1|CI680411
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|58657805|gb|CK046485.1|CK046485
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|88581492|gb|CI698483.1|CI698483
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|58687019|gb|CK075706.1|CK075706
EST:     CCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: CCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|2800921|gb|AA754215.1|AA754215
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|33796706|gb|CF324221.1|CF324221
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|88584252|gb|CI701792.1|CI701792
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|88578785|gb|CI687736.1|CI687736
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|88432901|gb|CI690757.1|CI690757
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|5003496|gb|AU068645.1|AU068645
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
EST: gi|2312262|gb|C28417.1|C28417
EST:     ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT
genomic: ACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaat ... tctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgatttgtgttgtcacgatttgcattactgatttcattctgtttctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTTGATGAGGCAGGGGCTTGGAAAAGCAAGCTTCAACCAGAATCCAGGCAAC
                           tactgat  putative branch site (score: 2)
                                 tttcattctgtttctt  CT-rich tract
                                atttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgacaatcttcattcacctgtgatttgtgttgtcacgatttgcattactgatttcattctgtttctttcctagGTTCAAAAACTCATTGCAGAATTGAATGAAATTTTGGCGCATGATGTTGTTGATGAGGCAGGGGCTTGGAAAAGCAAGCTTCAACCAGAATCCAGGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT