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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatttacatggaaaatactgttcttgtcaaattcctaatacttcgtagcatgtttcttctcttcatctgtttttattctaacgtgtgtttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTTTGCAGAGATTGCTGCTCTTCGATTCCTTAGTTCTCAG

Basic information

species Oryza sativa
transcript LOC_Os04g14654.2
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g14654.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G003734_T01 (Zea mays), 3'ss of exon 21
-------ttgcatttacatggaaaatactgttcttgtcaaattcctaatacttcgtagcat-gtttcttctcttcatctgtttttattctaacgtgtgtttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTTTGCAGAGATTGCTGCTCTTCGATTCCTTAGTTCTCAG
       | |  || | |||||||| | ||    |||   |     ||| |  | ||||||  |  |   | |  | ||| |||   |  ||  | ||||| |||||||||||| ||||| ||||||||||||||||| || |||||||| || || ||||| ||||||||||| ||||| ||||||||| | |||
aaacttatagtcttgatatggaaaacattgaaaatgtggga-----aattcccc-tagcattatcacagttataaacctgctttc--taaaatttctgtttattctagGGTTGGTCATCGCTCTCTGGTTTTGGTTGTATTCATTGGTGGTGTCACATTTGCTGAGATTGCTGCCCTTCGCTTCCTTAGTGCACAG

upper sequence: LOC_Os04g14654.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA10G35210.2 (Glycine max), 3'ss of exon 20
---ttgcattt-acat-ggaaaatactgttcttgtcaaattcctaatacttcgtagcatgtttcttctcttcatctgtttttatt--ctaacgtgtgtttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTTTGCAGAGATTGCTGCTCTTCGATTCCTTAGTTCTCAG
   || ||||| |||| ||    ||    | |  | |||||   | | ||| |  | |    | || |  |||| | ||| |      | || | | |  |       | ||||   ||| || ||||  | ||||||||| |||| || ||||| |||||||||||| |||| ||||||||  |  || |||||
ggtttacatttgacattggtgtgtaaaaatttgctgaaatttggagt-ctttgaggaagaaattttttaatcatttttttctggcacttcacatatttcagAGTACCTGATGGAAGGCGTGCTGTGGTGCTTGTTGTCTTTGTTGGGGGCGTTACCTTTGCAGAGATTTCTGCACTTCGATTTTTATGTACTCAG
















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|86866302|gb|CI336927.1|CI336927
EST:     AACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: AACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|86599219|gb|CI355836.1|CI355836
EST:     TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|88269427|gb|CI380725.1|CI380725
EST:     TCTTCATTGGATGTACACCAA-GTTT-GGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|88384593|gb|CI554085.1|CI554085
EST:     ATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGANATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: ATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|58603195|gb|CK013723.1|CK013723
EST:     TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|86846270|gb|CI339858.1|CI339858
EST:     TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|88273383|gb|CI393789.1|CI393789
EST:     TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|88460269|gb|CI529344.1|CI529344
EST:     CTTCATTGGATGTACACCAA-GTTTGNGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: CTTCATTGGATGTACACCAAGGTTTG-GGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|88250349|gb|CI348579.1|CI348579
EST:     TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGTTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
EST: gi|86432914|gb|CI093257.1|CI093257
EST:     TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAG                         GGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT
genomic: TCTTCATTGGATGTACACCAAGGTTTGGGGCTTCAACAGAGTATTGACAGgtaaattttc ... tttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtagcatgtttcttctcttcatctgtttttattctaacgtgtgtttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTTTGCAGAGATTGCTGCTCTTCGATTCCTTAGTTCTCAG
                                 ttctaac  putative branch site (score: 1)
                                             tttgttct  putative PPT
                         tgtttttattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatttacatggaaaatactgttcttgtcaaattcctaatacttcgtagcatgtttcttctcttcatctgtttttattctaacgtgtgtttgttctagGGTTGGACATCGTTCTCTGGTTTTGGTTGTCTTTATTGGTGGGGTTACTTTTGCAGAGATTGCTGCTCTTCGATTCCTTAGTTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
ttgcatt
- - - -tacatgg
- - - - - - - - - tactgtt