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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT

Basic information

species Oryza sativa
transcript LOC_Os07g46450.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G340359_T01 (Zea mays), 3'ss of exon 16
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
     | |  || | ||||||   |        | ||||||||    |||  |  || |||| |  | ||| ||||||||||||| | ||||||||| |||| |||||||| ||||||||||||||||||||||||||||||||| |||||||||| ||  ||
--gtgaggaaaagaatacatgcgcatc---agttcttgatttaggtgaatcttgcaacctaactatatatgtttctcagGCTAGAAGTAATGCAATCCTACAGGCAAGTTTAGAAAGAAGAAAACAAGCACTACATGAGCGCCGTGTGGCTCTGGAACAAAAT

upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G036872_T02 (Zea mays), 3'ss of exon 16
gtaca-aagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
|||   ||  ||| ||| |||||  |        | ||||||||    |||  |  ||  ||| |  | ||  ||||||||||||||| ||||||||| |||| |||||||||||||||||||||||||||||||| ||||| ||| |||||||||| ||||||
gtaaggaaaagaagagtgcatgtgcatc---agttcttgatttatgtgaatcttgcaacttaactatatat-tttctcagGCTAGAGGCAATGCAATCCTACAGGCAAGTTTGGAAAGAAGAAAACAAGCACTACACGAGCGTCGTGTGGCTCTGGAACAGGAT

upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 3'ss of exon 16
-------------------------gtacaaagggaatagtacatgtatactcaagacttttgatttacagta-atactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
                          |||||    |     | |  |||  | || |  ||| | | |    | |   |         |||       |   ||||| | |||||||||||| |||||||| ||||||||||||||||| ||||| |||||||| || ||  |||| || || || |||
tccttcaccttcagaccaatctctactacaagttaaccttaatagttatggtgaaaatgttttactcatgtcatacgttcgtggtcttttg-----attgaacagGCAAAAGGAAATGCAATTTTACAAGCTAGTTTGGAAAGAAGAAAGCAAGCTCTACATGACCGTCGGCTGGCCCTTGAACAAGAT

upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaa--actaa---ttggaaatgcttct---cagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
                | || | | ||   |||   |  |  |||  ||| ||  | |  |||||| | | |  | ||    |||| | |     |   ||||| | ||| |||||||| |||||||| || |||||||||||||| |||||  ||||||| || ||| |||| || || || |||
atcatcctgctccatattcagaagaaactttacccttcgatacaatgcttgtg--taaatgtaatattcacattattatattttggcattatgaataaacagGCGAAAGGGAATGCAATTTTACAAGCTAGCTTGGAAAGAAGAAAGCAAGCTTTACATGACCGTCGTCTGGCCCTTGAACAAGAT

upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ23838 (Selaginella moellendorffii), 3'ss of exon 15
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
                       |||||  |   ||  || |    |  |||| |    ||  || ||      || |||||| ||||||||||||  | ||||| |||||||||||| |||| |||||||| || || |||||  | ||||| || ||||| 
----------------------gtactcgcgttcttccatgtt--attgtactga----tatgtgcaag-----cttagGCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCACGATCGCCGGCTCGCTCTTGAACAGGAC

upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ24423 (Selaginella moellendorffii), 3'ss of exon 15
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
                       |||||  |  || |    |    |  |||| |    ||  || ||      || |||||| ||||||||||||  | ||||| |||||||||||| |||| |||||||| ||||| |||||  | ||||| || || || 
----------------------gtactcgcg--ttcttgcatgttattgtactga----tatgtgcaag-----cttagGCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCATGATCGCCGGCTCGCTCTTGAACAAGAC

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|58669247|gb|CK057933.1|CK057933
EST:     AAAGACTGGAGATCACAAAGAATGACCTCCAGATCAGAATCGCGAAAGAG                         GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCA
genomic: AAAGACTGGAGATCACAAAGAATGACCTCCAGATCAGAATCGCGAAAGAGgtacaaaggg ... tgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
                                             tgcttctc  CT-rich tract
                      taatactaaaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG