Sequence
atgc intronic sequence ATGC exonic sequence...tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g09140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 2
tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaag-gaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
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-caaaactgctgctactatcttttctaggagtacctgttactcaagctttctgaatgagagaaacttgaaatgtgttcacttacatgtcttttgtgcacagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 2
tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
| || | | || || | || | || | || || |||||||||| || |||||||| | |||||| ||||||||||| || |||||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||| ||||||||||| ||
-------tgct--actatcttttctaggagtacctgttactcaagctttctgaatgagagaaacttgaaatgtgttcacttacatgtcttttgtgcacagtgattgtagGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 2
tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaagg-----------aaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
| || ||| | ||| | || ||||||| | || |||| ||| | | |||||||||||| ||| | |||||| ||||| ||||||||||| || |||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||
-----tgcacagaa-ctgctgctacaaccttttttagg-agaacatgttactgaagctttctgaatgaaagaaacttga--aatatgtacgtacatgtgttttgt--acagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCTGCTATTCTTGTCACTCCTCTTGGTGCACTCAGTATAATCATCAG
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G34470.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------tctaatatactgaagttactgtttcatttgtttttagacaa-----aaaatgtcactaaggaaagaaacttgactaatg--------gcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
|| || | | | | | ||||| || || | | | | | || | | || | | ||| | | | | || | |||||||||| || |||||||| ||||||||||||||||| ||||| ||||| ||| | || ||||||||||| || ||||| ||||| |||||
gtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgttgatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 2
tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
| || || ||| || | ||| | | | |||| | ||| | | || || | | | | ||||| | | || |||||||| ||||| ||||||||||||||||| |||||||| ||||| |||||||| || || ||||||| || |||||
----gtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttgg-tttgttttgttgc-tcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------tctaatatactgaagtt--actgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatgg----catcttacatgacctttgtga-acagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
| | | |||| ||| |||| || || | || | | | || | || | | | |||| || | || | ||||| |||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| |||||||||||||| || || || || || |||||
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcactaaggaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
cctttgt CT-rich tract
aaagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC