Sequence
atgc intronic sequence ATGC exonic sequencegtatgaaagacacagaaatgcttcaacctgtgcgatttttttatcgtattgttatttgacaactaactaactaaccatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g47490.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G082385_T01 (Zea mays), 3'ss of exon 6
--gtatgaaagacacagaaatgcttca-acctgtgcgatttttttatcgtattgttatttgacaactaactaactaaccatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
| | | | ||| || || |||| || ||||| | || | || | | | ||| | ||| ||| | | |||| | ||||||||| ||||||||||| ||||| |||||||| || | || ||||||||||| ||||||||||| ||| |||| || || || ||||| ||||| ||||
gtatgtagattaaacaaaattgtttcatacttgtgcaaagttacatatatgttataact----aacca--taattaatcgagaactttgttatttcagGGCCTAGACACAATGGTCGGTGAGCATGGAGCACAATTGTCAGGAGGGCAAAAACAAAGAATTGCAATCACAAGGGCAATACTGAAAAACCCCAAGATCT
upper sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------------------------------gtatgaaagacaca-gaaatgcttcaacctgtgcgatttttttatcgtattgttatttgacaactaactaactaaccatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
| | |||| | ||| | | ||| || | | | || || | | || ||| | ||| || ||||| |||||||||||||| |||||||||||| | ||| |||||||||| || |||||||||||||| || |||||||| || | || ||||| | ||||
gtgagcctatgattcattcatattcaggtcacagttgaaagagggttcaaatatacatgtctgttagaatgagtccatgaatcactgcatttcaacctcacagacctttgtaataataagagtcatgcaatcaaacaaattcttctcttcttttcatcagtattttgaatcatgg-tggtgtgtttacagGGGCTGGACACAATGGTGGGTGAACATGGAACGCAGTTATCTGGAGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAATCCAAGAATCC
upper sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------------------gtatgaaagacacagaaatgcttcaacctgt------gcgatttttttatcgtattgttatttgacaactaactaacta-accatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
| |||| | | |||| |||| | ||| | || || | | | |||| | || | | | | ||| | ||||| || ||||||||||| |||||||||||| ||||||||||||| || || |||||||||||||| || |||||||| || | || || || ||||
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaat-cttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
upper sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------------------------gtatgaaagacacagaaatgcttcaacctgtgcgattttt-ttatcgtattgttatttgacaactaactaactaaccatc-tcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
| || || || | | | | ||| ||| || || || | || | | | ||| | | | | | | | | ||||| || ||||||||||| ||||| |||||| ||||||||||||| || || |||||||||||||| || |||||||| || | || || || | ||||
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtcta-aacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
upper sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0003g02550.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------gtatgaaagacacagaaatgcttcaacctgtgcgatttttttatcgtattgttattt-------gacaactaactaactaaccatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
| || ||| | | | | |||||| || ||| | |||| | | ||||| | | | ||| | | | | | | || ||||| | || |||||||| ||||| |||||| ||||||| |||| ||| || |||||||||||||| || ||||| || || || || || || | ||||
gtgagcccattctttcttttgtgggattccattatatccaggcattcatctactgttctgttaga-attgtactaattcaacttgacacctttctctatcacaatactattttcttctgatcttttgagtaattggactgttgtggtctgttaacagGGGATTGAAACAATGGTGGGTGAGCATGGAACTCAGCTCTCTGAAGGACAGAAGCAAAGAATTGCAATAGCAAGGGCCATTCTGAAGAACCCAAGAATCC
upper sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
gtatgaaagacacagaaatgcttcaacctgt------gcgatttttttatcgtattgttatttgacaactaactaacta-accatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
|||| | | |||| |||| ||| | || || | | | |||| | || | | | | ||| | ||||| || ||||||||||| |||||||||||| ||||||||||||| || || ||||||||||||
-ctagaaaaagttacaaat-cttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcgtattgttatttgacaactaactaactaaccatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
aactaac putative branch site (score: 1)
ccatctcttctgtttt CT-rich tract
tattgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaaagacacagaaatgcttcaacctgtgcgatttttttatcgtattgttatttgacaactaactaactaaccatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA