Sequence
atgc intronic sequence ATGC exonic sequence...ttgaacatgcttgaatatttttatttatgcttgttatatactacagtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g44330.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 8
----------------------------------------------------------------------------------ttgaaca----tgcttgaatat--ttttatttatgcttgttatatactacagtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
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gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaaactattttttggatatgctgtcatttcattcttttacgcacaaaatgcacaataccaat--ttaacaccatttatgtgtccattgcttg-tattct--agGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G151236_T03 (Zea mays), 3'ss of exon 7
----ttga-acatgcttgaatatttttatttatgcttgttatatactacagtcattgtatctacagtaaacatcctttttaattttttgtcttgat-attctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
|| | | | ||| | | | ||| | | | ||| || | | | | | |||| | ||| | | | | | ||| | | | |||||||||||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||||||||
cttcttaatataagctcgggggctgt--cttacccccgcagg----tcgagttttttttttttaaattaacaccgtttattactgtgtccattgcttgtaccctagGTGAATGAGGCTAAGAATGTGCTCAAGCTATGTGATTTTGGGAATGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTTAGCCGTTTCTATC
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
ttgaacatgcttgaat-atttttatttat-gcttgttatatactacagtcattgta---tctacagtaaacatccttt---------ttaattttttgtcttgatattct--ttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
|||| | ||| | | || | | | | ||||| | ||| | || || | | ||| ||| || ||| || || || | || | | |||| |||||| |||| ||||| ||||||| ||||| ||||||||||| ||| ||||||| | || || |||||||| ||||||||||| ||||| ||||
----gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaagaaatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
-----ttgaacatgcttgaatatttttatttatgcttgttatatactacagtcattg-tatctacagtaaacatcc--tttttaattttttgtctt--gatattcttt-------agGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
|| || || | ||| ||| | ||| | | | | | | || | || | | ||| ||| ||| ||| ||| || | || | || | |||| ||||||||||||||||| ||||||| ||||| ||||| ||||| ||| ||||||| | || || |||||||| ||||||||||| ||||| ||||
gtatgcctaaaatactgttgtgtttagattgtttcttttca-aaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G25840.1 (Arabidopsis thaliana), 3'ss of exon 8
ttgaacatgcttgaatatttttatttatgcttgttatatactacagtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
| | | | ||| | || | | | || || | | || | | || | | | || ||||| ||| | |||| ||||||| || ||||| | ||||| ||||||||||| ||||||||| |||| || | ||||| |||||||| |||||||| || || || ||
-------------------gtcagtcacacttttcattggtt----ttctcctactta-attcaatagctttctaactgttgggtctttg-attgtccagGTCAATGAGGGGAAAAATGTCTTAAAGCTTTGTGATTTTGGTAATGCAATGTTTGCAGGCAAAAACGAAGTTACACCGTATCTTGTTAGTCGCTTTTACA
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 8
-------ttgaacatgcttgaatattt--ttatttatgcttgttatatact-acagtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
|| | || ||| || | || | | ||| | || | | || | | || | || | | | ||| ||| || || |||| |||||||| || ||||| ||||| |||||||||||||| ||||| ||| || |||| | || || ||||||| |||||||||||||| || ||||
gtaggttttaagtatacttttatgtccagttgcctgccttagttttttatttgttataataaattttgcattgaattttactatatattcattgcct------ctttcagGTAAATGAGGCCAAAAATGTCCTGAAACTCTGTGATTTTGGTAATGCCATGTTTTCTGGTAAAAATGAAATTACACCATATCTTGTGAGCCGCTTTTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
tattcttt CT-rich tract
tttttaattttttgtc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaacatgcttgaatatttttatttatgcttgttatatactacagtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC
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