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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttacaagttttggtaattgcacatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaattgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g36860.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G077125_T01 (Zea mays), 3'ss of exon 5
-cttacaagttttggtaattgcacatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaat--tgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
| ||| | | || ||| | ||| ||| | | | | || || |||| ||| || | | ||||| || |||||||| |||||||| ||||| ||||||||||| ||||||| ||||||||| ||||||||||||| ||||||||||||||||||||||| || ||||| |||
gaatctcagtccagtttgtttcactt---catatgtgcttgcgggtcctttcggtcagaattcacataaaaataatggagcatttcatgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTATGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT

upper sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
ctta--caagttttggtaattgcacatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaat--tgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
|||| | ||||| | ||| | | | | ||||| || | | ||| ||| ||| | |||| | ||| ||||| || |||||||| |||||||| ||||| ||||||||||| ||||||| || |||||| ||||||||||||| ||||||||||||||||||||||| || ||||| |||
cttagtccagtttgtttcattttatctgtgcttttgtgg----gtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT

upper sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
----------------ctta-caagttttggtaattgc-acatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaattgaattgact-tctgtttcattggc------------acagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
||| || ||||| | ||| | | || | || | || || ||| || || || | | | | | | || || || | |||||| || |||||||||| ||||| || || | |||||||||||||| ||||||| ||||||||||| ||||| |||||||| | || || || ||
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccact--gtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC

upper sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
--------------------------cttacaagttttggtaattgcacatttacatttgtacctat----gtgcatcacgtgttg---acgtttacattttaattga-attgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
|| || || || | |||| | || | | || ||| | || ||| || |||| | |||| | ||| |||||| || |||||||||| ||||| || || | |||||||||||||| ||||||| ||||||||||| ||||| |||||||| | || || || ||
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttg---cagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC

upper sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
cttacaagttttggtaattgcacatttacatttgtacctatgtgcatcacgt-gttgacgtttacattttaat--tgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
| |||| | ||| | | | | | | | || | | | | ||| || |||| | | |||| ||| | || |||||||| || ||||| ||||||||||| ||||| | || |||||||| ||| ||||||| |||||||| ||||| ||||||||||| || || || || ||
-gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgac--ctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC

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|29644769|gb|CB649776.1|CB649776
EST:     TTGGTTGCAACAGATGTTGCTGCACGAGGCTTAGACATCAAAGATATCAG                         GGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCG
genomic: TTGGTTGCAACAGATGTTGCTGCACGAGGCTTAGACATCAAAGATATCAGgtactccatc ... attggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCG
EST: gi|29627752|gb|CB632763.1|CB632763
EST:     TTGGTTGCAACAGATGTTGCTGCACGAGGCTTAGACATCAAAGATATCAG                         GGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCG
genomic: TTGGTTGCAACAGATGTTGCTGCACGAGGCTTAGACATCAAAGATATCAGgtactccatc ... attggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCG
EST: gi|29646239|gb|CB651246.1|CB651246
EST:     TTGGTTGCAACAGATGTTGCTGCACGAGGCTTAGACATCAAAGATATCAG                         GGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCG
genomic: TTGGTTGCAACAGATGTTGCTGCACGAGGCTTAGACATCAAAGATATCAGgtactccatc ... attggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacgtgttgacgtttacattttaattgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
                             aattgac  putative branch site (score: 3)
 tttcatt  putative PPT
 tttacattttaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttacaagttttggtaattgcacatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaattgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - -gcacatt
- - - - - - - - - - - - - -acatttg
- - - - - - - - - - - - - - - - - - - - -gtgcatc
- - - - - - - - - - - - - - - - - - - - - - - - -cgtgttg