Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaattttaactgcttggtttattagttccagtttcatgtcgaacaattcgttaccctgtcttgaaaaaacttttaggtatttctgactgattatcgatgggttgttggccttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGACTTCCACACCGACTGCGTCAAGAAGTGGTTGAAGGAGAAGAACTCATGCC

Basic information

species Oryza sativa
transcript LOC_Os01g06590.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G305901_T01 (Zea mays), 3'ss of exon 6
gtacaattttaactgcttggtttattagttccagtttca--tgtcgaacaattcgttaccctgtcttgaaaaaacttttaggtatttctgactgattatcgatgggttgttggccttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGACTTCCACACCGACTGCGTCAAGAAGTGGTTGAAGGAGAAGAACTCATGCC
       | ||  | |||     |   ||||| |||  |  || | || | |     ||| || ||    ||| || || |    |||||  || | | ||||||||     || || || ||||||||  |||| ||||||   | ||||||| |||||||||||||  |||||||||||| ||| |||| ||||||||||| || ||  ||||||||| ||||
------gtatacatactttcgcaacatgttcctgttaaagatgcctaatactattcaaccatggctc---aaagctgttgga---ttctg-ttgctgaccgatgggt-----gcattctg-gcagGAGGGTTACAGAGACAAGGATATGCTGGGGATACTGAAATGCAGGCACGACTTCCACGCCGGCTGCATCAAGAAGTGGCTGCAGACGAAGAACTCGTGCC

upper sequence: LOC_Os01g06590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G165044_T01 (Zea mays), 3'ss of exon 6
gtacaatt--ttaactgcttggtttattagttccagtttcatgtcga-acaattcgtt--accctgtcttgaaaaaacttttaggtatttctgactgattatcgatgggt-tgttggccttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGACTTCCACACCGACTGCGTCAAGAAGTGGTTGAAGGAGAAGAACTCATGCC
||| | ||  | ||   | |   |  | |   |  | ||  |  |   || | ||  |  ||| || |     ||| ||  | |    | ||  ||  | | ||| || |  ||| |      |  |||||||| |||| ||||||      |||||||||||| || ||||  |||||||||||| ||| |||| ||||||||||| || ||  ||||||||| ||||
gtatatttcatcaaacacgttcctgttaaagacacgcttattaccattactactcactcaaccatggcccccgaaatctgctggactctactt-ctactgaccgacggatgcgttcgttccccg-acagGAGGACTACAGAGACAAGGAGGCGCTGGGAATACTCAAGTGCAGGCACGACTTCCACGCCGGCTGCATCAAGAAGTGGCTGCAGACGAAGAACTCGTGCC
















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|29670363|gb|CB666638.1|CB666638
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88530273|gb|CI458653.1|CI458653
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|29629980|gb|CB634989.1|CB634989
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|33682425|gb|CF310664.1|CF310664
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|7839249|gb|AU090660.1|AU090660
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|86842401|gb|CI335289.1|CI335289
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|29622198|gb|CB627209.1|CB627209
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88548851|gb|CI478682.1|CI478682
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88288960|gb|CI520290.1|CI520290
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|29669273|gb|CB665548.1|CB665548
EST:     TTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTTTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|3760896|gb|C98150.1|C98150
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88281237|gb|CI402435.1|CI402435
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88550098|gb|CI480041.1|CI480041
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACCACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88851069|gb|CI373827.1|CI373827
EST:     GTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: GTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88830640|gb|CI078084.1|CI078084
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88470128|gb|CI407399.1|CI407399
EST:     CTGATGAACAGCCAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|29684935|gb|CB681210.1|CB681210
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88437813|gb|CI533770.1|CI533770
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88539715|gb|CI469695.1|CI469695
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|3760897|gb|C98151.1|C98151
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|7839221|gb|AU090632.1|AU090632
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|29623670|gb|CB628681.1|CB628681
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88993479|gb|CI110300.1|CI110300
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88489480|gb|CI426752.1|CI426752
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
EST: gi|88527686|gb|CI455863.1|CI455863
EST:     CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTG                         GAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC
genomic: CTGATGAACAGCAAAATGATCAAGATGATGGGAAATGTGCAATTTGTCTGgtacaatttt ... ttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacttttaggtatttctgactgattatcgatgggttgttggccttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGACTTCCACACCGACTGCGTCAAGAAGTGGTTGAAGGAGAAGAACTCATGCC
                                           ccttttgt  CT-rich tract
            tatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaattttaactgcttggtttattagttccagtttcatgtcgaacaattcgttaccctgtcttgaaaaaacttttaggtatttctgactgattatcgatgggttgttggccttttgtgcagGAGGAATACAAAGACAACAGTTTGCTGGGAATACTGAAATGCAATCACGACTTCCACACCGACTGCGTCAAGAAGTGGTTGAAGGAGAAGAACTCATGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC