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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os07g14270.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 8
gtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG
||||  || |||  ||||||||  ||||    | |  | | ||  | | ||  | | |   | ||||||  | |   || || |||||||| |||||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||| ||||||||
gtatgtttccctgaaattgaac--cttgtatcttcttactatttggttattagaatattagtgctgaacc-tatgtcttatgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTGGCATTGAGCTGTGGCAG

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------------------gtataattgccttt-aattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG
                                                                               |     |    ||| || | ||   |     || | | |      ||    |  | | |   | ||||| | |     |||||  ||||||| || ||||||||||||||||| || || || |||||| |||||||||||||||||||| ||||||||
gtatgtttgcctgaaacggatccttatatcttcttactgtttggctattactacgtcccttctcgaatatttgtggctcgctagttcatttttgaactaaaacgcgacaaataaaaaagaaaggagggagtagaatgttagtgctgaa-tctaattcttgtgcatcacagATTTTAAGGATGATCCATACATTTACGCCTTCGACAGCTTGAAGTACATTGGCATTGAGCTGTGGCAG
















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|88729754|gb|CI753264.1|CI753264
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTG
EST: gi|29629339|gb|CB634350.1|CB634350
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29623310|gb|CB628321.1|CB628321
EST:     AGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: AGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|286955|gb|D15762.1|D15762
EST:     CGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: CGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|163920423|gb|EG710621.1|EG710621
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCT
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCT
EST: gi|33793505|gb|CF322636.1|CF322636
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29658654|gb|CB654929.1|CB654929
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|88718533|gb|CI742043.1|CI742043
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTT
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTT
EST: gi|88722171|gb|CI745681.1|CI745681
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGC
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGC
EST: gi|89182828|gb|CI045586.1|CI045586
EST:     ACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: ACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|86593321|gb|CI257961.1|CI257961
EST:     CCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: CCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|11610430|gb|AU166106.1|AU166106
EST:     TAACTACCAAGGCCAAATGGAAGNCACCGATGATCGACANCCNAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: TAACTACCAAGG-CAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|88691187|gb|CI735266.1|CI735266
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAG
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     AACCCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTG
genomic: AACCC-TAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTG
EST: gi|396941542|gb|HO188751.1|HO188751
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|14192066|gb|AU184277.1|AU184277
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|15851813|gb|BI800089.1|BI800089
EST:     ACTACCAA-GCAAATGGAA-GCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: ACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29662654|gb|CB658929.1|CB658929
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|86497286|gb|CI139919.1|CI139919
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCNTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29644253|gb|CB649260.1|CB649260
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|33793940|gb|CF322858.1|CF322858
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|88690114|gb|CI734193.1|CI734193
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCAT
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCAT
EST: gi|88730078|gb|CI753693.1|CI753693
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTAT
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTAT
EST: gi|29673077|gb|CB669352.1|CB669352
EST:     GAACCTTATCTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAAACCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|8856749|gb|AU094067.1|AU094067
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|58592538|gb|CF990846.1|CF990846
EST:     GAACCCTAAGTAGCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29662655|gb|CB658930.1|CB658930
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|88996495|gb|CI259999.1|CI259999
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|86600080|gb|CI258420.1|CI258420
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|86255007|gb|CI017127.1|CI017127
EST:     GCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|3760360|gb|C97614.1|C97614
EST:     G-ACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGAC-ACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|87042082|gb|CI194706.1|CI194706
EST:     TGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: TGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29663170|gb|CB659445.1|CB659445
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|8528286|gb|AU093101.1|AU093101
EST:     G-ACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29660493|gb|CB656768.1|CB656768
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29660220|gb|CB656495.1|CB656495
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|29629338|gb|CB634349.1|CB634349
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|58679227|gb|CK067914.1|CK067914
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
EST: gi|86481114|gb|CI123747.1|CI123747
EST:     ATGATCGACAACCCAG                         ACTTCAAGGATGATCCGTACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: ATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG
                                    tttcctttgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG