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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacag

Basic information

species Oryza sativa
transcript LOC_Os07g14270.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttc---ctttgtggttcacag------------------------------------------------------------------------------
|||||||||||||| |||||||| || |||||||||||||| ||||| ||||||||||||||  ||||||  ||  || |  |||     | |  | | ||  | | ||      | | ||||  | | |||    ||   | |||||                                                                                 
AAAATCAAGAACCCGAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttgcctgaaacggatc--cttatatcttcttactgtttggctattactacgtcccttctcgaatatttgtggctcgctagttcatttttgaactaaaacgcgacaaataaaaaagaaaggagggagtagaatgttagtgctgaatctaattcttgtgcatcacag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacag
||||||||||||||||||||||| || |||||||||||||| ||||| ||||||||||||||  || |||  ||||||||  ||||    | |  | | ||  | | ||  | | |   | ||||||  | |   || || |||||||
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttccctgaaattgaac--cttgtatcttcttactatttggttattagaatattagtgctgaacc-tatgtcttatgcttcacag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaac-tgtttcctttgtggttcacag-------
|||||||||||||| |||||  |||| ||||||||||||||  |||| || ||||||||| | |||        ||  |||   | |||  | |  | | | |  | ||   | ||  |   | ||  | ||     | ||    |||        
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgt-tcattatacgcccttctacacagtagta--atatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G28890.2 (Glycine max), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaac-tgtttcctttgtggttcacag-------
|||||||||||||| |||||  |||| ||||||||||||||  |||| || ||||||||| | |||        ||  ||| | | |||  | |  ||| | |  | ||   |  |  |   | ||  | ||     | ||    |||        
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgt-tcattatacactcttctacaccgtagta--atatttttataaattattttgcattataagataaatatattcaacatttgaaaaacatttgtcag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaa-ttgaacaacttggtat-tacacatttttca-gatgttgaactctgcattctga-actgtttcctttgtggt-tcacag-------------------------
 |||| || ||||| |||||| | || |||||||||||||| ||||| ||||||||||||         ||  | || ||||  ||  | | |   || | ||   | | || ||   |   |||| | |||| |   |||      ||  |                          
CAAATAAAAAACCCCAACTACAAGGGAAAATGGAAGGCACCTATGATTGACAACCCAGgttcttgcatattccacttcaacattttaatttgtttgcagtcttggtgttctttaatgttattttctaatactgatatattttcaacatcttaaatttgtgtgttttttgcctttttag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctga-actgtt---tcctttgtggttcacag
||||| ||||| || |||||| | || |||||||||||||| ||||| |||||||||||| |  |  || |  |         |   |   | |  | |||      |||  |||  ||||| || |||  |      ||  |  || ||||
AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgt-tcctatccatgcacctgcttcttctatgccatagttattttttggtttggtctcaacattcagacacttataaactgttcatattttacag

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|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|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|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|14192066|gb|AU184277.1|AU184277
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|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|58679227|gb|CK067914.1|CK067914
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 68 (downstream exon)
Score: 367

AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacag

- - - - - - - - - - - - - - - TGGAAG