Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTGGCATTGAGTTGTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os07g14270.1
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|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|58679227|gb|CK067914.1|CK067914
EST:     GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG                         ACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
genomic: GAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgc ... tggttcacagACTTCAAGGATGATCCATACATCTATGCTTTTGACAGCCTGAAGTACATTG
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


 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