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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaagaaaaaaaacagacaattaagggccaactgtttttttttaacggatatctcctactggccagtctaaatttgggaaatataatttcaaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGG

Basic information

species Oryza sativa
transcript LOC_Os03g49600.5
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 6
gaaagaaaaaaaacagacaattaagggccaactgtttttttttaacg-gatatctcctactggccagtctaaatttggga--aatataatttcaaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGG
   |   || |  ||| |  |  |          | | | |  |||  || |  |   |       || |||||||  ||  | | |  |||  ||||||||||| |||||| |||| || ||||||||||||||||||||||||||||||||||||||  | |||||||| |||||||||||||||||||||||||| ||||
---atgcaatagccagcctgtccaatttgctagatatatgtacaacttgacaattaacatattattgtttaaatttctgatgattttttttttcaaaatgtagGCTGCTCAGAAAGGAAAGGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTCACAAACTCAACCGAAGACCAAGCAGCGGCTCAAAGAGCAAGGG

upper sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118003_T01 (Zea mays), 3'ss of exon 6
gaaagaaaaaaaacagacaattaagggccaactgtttttttttaacggatatctcctactggccagtctaaatttgggaa--atataat--ttcaaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGG
              | || |||         |   |    ||| |    | |||   ||||   | |    ||    ||   | || ||  || |||||  ||||| |||||| | || || || |||||||| ||||||||||| ||||| || |||||| | |||||| |||| ||||||||||| || |||||||||||||
----ttgttctcctaaacgattggacatgtgcctgtcgaatttcattagtttcttggactgaaaactgctgatggaagagtgacatgatgttttaaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGG
















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|218498123|gb|FG968220.1|FG968220
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|58676021|gb|CK064708.1|CK064708
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|32948487|gb|BP185059.1|BP185059
EST:     TTCTCTTATCACATGCTGCAACTGTTGCAAGAT-CCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAA-GTTGGAATAGTTCTGGACTTCAATTGGTATGA
EST: gi|33381892|gb|CF197235.1|CF197235
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGNTACCGGACTAAGTATCNN                         NCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|58677218|gb|CK065905.1|CK065905
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTT
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTT
EST: gi|33794165|gb|CF322973.1|CF322973
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|88212028|gb|CI211668.1|CI211668
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|40490189|gb|BX899802.1|BX899802
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|58681508|gb|CK070195.1|CK070195
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|33795224|gb|CF323484.1|CF323484
EST:     TCTCTTATCACATGCCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCA-GGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TCTCTTATCACATGC-TGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|2311685|gb|C27840.1|C27840
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|58662457|gb|CK051143.1|CK051143
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|3106636|gb|D42356.1|D42356
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|428803|gb|D24959.1|D24959
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCA-GGCAAAGTTGGA-TAGTTCTGGACTTCAATTGG-ATGAG
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|86910403|gb|CI293058.1|CI293058
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|58682166|gb|CK070853.1|CK070853
EST:     TCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCGAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGA
genomic: TCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATC-AGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGA
EST: gi|58682361|gb|CK071048.1|CK071048
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|33674893|gb|CF303132.1|CF303132
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
EST: gi|58680358|gb|CK069045.1|CK069045
EST:     TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAG                         GCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA
genomic: TTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttttc ... aaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggatatctcctactggccagtctaaatttgggaaatataatttcaaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGG
                    gtctaaa  putative branch site (score: 3)
                       taaatttgggaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaagaaaaaaaacagacaattaagggccaactgtttttttttaacggatatctcctactggccagtctaaatttgggaaatataatttcaaaaatgtagGCAGCTCAGCAAGGCAAAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA