Sequence
atgc intronic sequence ATGC exonic sequence...gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g17080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 4
---gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcc--tggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
| | | || | |||| || | || || ||| | |||| |||| ||| || ||||| | || ||||| ||||| || ||||| ||||| ||||||||||| || ||||| ||||||||||||||||| ||||||||||||||||| ||||| ||||| || |||||| | |
atagttactgcttactttgtagt--caaataaaaaaaatggttgctagtgtttgtgaaatgaagatggataatcaatgt-tgttataatcttt--tttctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttg-----cagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
|||| | | | | || || ||| | | | || |||||| | ||| ||| | | ||| | ||| ||||| |||||||| ||||| ||||||||||| || ||||| |||||||||||||| || ||||||||||||||||| ||||| ||||| || |||||||| |
--tggacaatgtttctatgcttctgtgtaccataatgatttattatct-tatcccggacctggact--tggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
----gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
| |||||| | | | || || ||| | | | | || | | | || ||| || | || ||||| |||||||| ||||| ||||||||||| || ||||| ||||| |||||||| || ||||||||||||||||| ||||| ||||| || |||||||| |
tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttg----tttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
gcaatgaaatgctgtctagttccagttgctggctat--atttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaat-tcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
| || | | | | || | || |||| || || | || | | | || | || || | | || | |||| ||||| || ||||| ||||| ||||||||||| || ||||| || |||||||||||||| ||||||||||||||||| ||||| ||||| || |||||| | |
--taggagttattttatccctctaacca-tgcctattaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------gcaatgaaatgctgtctagt-tccagttgctgg---ctatatttttct--ttgtacatataatgcctgg-agtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
| || | | | || ||| | | ||||| | ||| || ||||| | ||| | | | | | | | | ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||| | |
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtat--cggtgaaccttatact-gttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
|||| |||| | || ||| | | || ||| || |||| | | | || | | | | | || || ||||| |||||||||||||||||||||||||| || ||||| |||||||| |||||||| ||||||||||| || || || |||||||| || || ||| | |
-tcatgattcagtgtcca--tcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ31453 (Selaginella moellendorffii), 3'ss of exon 3
gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
|| ||| || | | ||| | |||| | || || |||| | ||||||||||||||||||| ||||| ||||| || ||||| ||||| || ||| | || |||||||| || ||||| || || || || || || || ||| | |
----------------------------gtgattatgacattg-----aagtgtaa--ctgcaagtagagtctaatgtt-tactttgtgg---tctgcagTACACACCAGCAATTGATATCTGGAGTATTGGTTGTATATTCGCTGAAATCTTGACAGGAAAGCCGCTTTTTCCTGGAAAGAACGTAGTACACCAATTAGMapped 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|117237171|gb|CT861779.1|CT861779EST: CAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG TACACACCAGCAATAGATATATGGAGCATCGGTTGCATA
genomic: CAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAGgttagtcacc ... attcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATA
EST:
gi|58600533|gb|CK011061.1|CK011061EST: CAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG TACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTT
genomic: CAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAGgttagtcacc ... attcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
ttcttgc CT-rich tract
atataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
-caatgaaa
- - - - -tgctgtc
- - - - - - - - - - - - - tgctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgtt