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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacaactgaaacaaaaactaagtcaaagtagtaacacattttttttgaggttcaactcaccaagaatcatctttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG

Basic information

species Oryza sativa
transcript LOC_Os11g35400.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 16
------gtatgacaactgaaacaaaaactaagtcaaagtagtaacacattttttttgaggttcaactcaccaagaatcatctttgaatc---agGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG
        |  ||| |  |||| |||| |   |  | |     |      ||   |   |     | | |    |   |  |  |||||   |||| |||||||| || |||||||| ||||| ||||| ||||| |||| ||||||||||| ||||||  | ||||| ||||| |||   |||| |||| | |
gtacgccgacaacaccctaaaccaaaattgttttcatgctccgatttggcttacctagaggatggc-cgctcctacctacgtacgaatctgcagGTCTGGGTCTACGGGAACAGCTTCGAGTCGTTCCTCGTTGCCGTGGCTGTCCCTGAGAGGCAGGCTCTCGAGGAATGGGCAGCAGCCAACAGCAAGGCCG

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA20G01060.1 (Glycine max), 3'ss of exon 16
----------------------------------------------------------------------------------------gtatgacaactgaaacaaaaactaagtcaaagta--gtaacacattttt----tttgaggttcaactcaccaagaa-tcatctttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG
                                                                                           | ||  |  ||  |       |||  |  ||   ||  | |||| |    ||  |  ||  |   |  ||||| | || |   |  ||| ||||||| |||||||||||||||||||| ||| | || ||||| || |||||||| |   | |||||||||||||||||   | |  ||||   |||||
gtatgcttctagttcaatcacaacagttgataaaagtagagaaacaatagttatagttcatttttggtcatattaagtttactgggaaagtttacttcgaaagtagttttgcagtgcacctattatactaaatttgtgtaattaaatattggataaaaaaagaaattatttcacatgcagATTTGGGTGTATGGAAACAGCTTTGAGTCATTCTTGGTGGCTGTTGTGGTCCCTGAAAGAAAAGCCATTGAGGATTGGGCAAAAGAGCACAATTTGACTG

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA12G05140.1 (Glycine max), 3'ss of exon 16
-----------------------------------------------------------gtatgacaactgaaacaaaaactaagtc--------aaagtagtaacacattttttttgag-gttcaactcaccaagaatcatctttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG
                                                           | ||  ||  ||      |  |  |||         ||||| |    |||  |   |  |   || || | |   | ||| ||     |  ||| ||||||||||||||||||| ||||| || ||| | || || ||||| |||||||| |   ||||| ||||||||||||| |   |  | ||    || |
gtatgtttctgcttcaagcatagaacattcagtaaaattagagcaacattaattgcattgcattgcatttgtgttggatgcctagttttgtagggaaagtggacttacaaatagctcaactattaaatttatgtataat-attccatatgcagATTTGGGTCTATGGAAACAGTTTTGAATCTTTCTTGGTGGCAGTGGTGGTCCCTGAAAGAAAGGCCCTTGAGGATTGGGCAGTGAAGCATAATTCTACAG

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv03s0063g01880.t01 (Vitis vinifera), 3'ss of exon 16
------------------------gtatgacaactgaaacaaaaactaagtcaaagta-gtaacacattttttttgaggttca--actcaccaagaatcatctttgaat---cagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG
                           ||| | ||  |  || |  || || |   || || || ||| ||| |  |  ||||  | |   |   | |  |||     |   ||| ||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| || ||  ||||  ||||||||||||| | | |  | ||   |||||
gtatgttgattagtttttatagaaagctgatatctacagtaacatttatgttagcatatgttac-catctttctctactttcataatttctctttacttttctgctggtgctcagATTTGGGTCTATGGGAACAGTTTTGAGTCTTTCCTTGTTGCTGTGGTGGTCCCGGATAAAAAGGCACTTGAGGATTGGGCAGAAAACCATAATGTGACTG

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|58679886|gb|CK068573.1|CK068573
EST:     CAGTGGAGGTCGTGGAAAGCGCATACGTGCAGTCTCCTCTCGTTACATCA                         GTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
genomic: CAGTGGAGGTCCTGGAAAGCGCATACGTGCAGTCTCCTCTCGTTACATCAgtatgacaac ... tttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
EST: gi|66947111|gb|AU311955.1|AU311955
EST:     CAGTGGAGGTCCTGGAAAGCGCATACGTGCAGTCTCCTCTCGTTACATCA                         GTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
genomic: CAGTGGAGGTCCTGGAAAGCGCATACGTGCAGTCTCCTCTCGTTACATCAgtatgacaac ... tttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
EST: gi|86501811|gb|CI144444.1|CI144444
EST:     TCCTCTCGTTACATCA                         GTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
genomic: TCCTCTCGTTACATCAgtatgacaac ... tttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
EST: gi|86501867|gb|CI144500.1|CI144500
EST:     CAGTGGAGGTCCTGGAAAGCGCATACGTGCAGTCTCCTCTCGTTACATCA                         GTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC
genomic: CAGTGGAGGTCCTGGAAAGCGCATACGTGCAGTCTCCTCTCGTTACATCAgtatgacaac ... tttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagtaacacattttttttgaggttcaactcaccaagaatcatctttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG
                                        tcatcttt  CT-rich tract
     taacacatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacaactgaaacaaaaactaagtcaaagtagtaacacattttttttgaggttcaactcaccaagaatcatctttgaatcagGTTTGGGTCTATGGAAACAGCTTTGAGTCCTTCCTTGTTGCTGTGGTTGTCCCTGAGAAGCAGGCCATTGAGGATTGGGCTGCACAAAACAACAAGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT