Sequence
atgc intronic sequence ATGC exonic sequencegtgagatggtgacctatgctgtgaaatgtatgcacatttttggtgctagattgttctgcaacagtaactctaaagaacttcactattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCATTAAAAATTCAGCAGTTCAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g48200.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 2
-------gtgagatggtgacctatgctgtgaaatgtat---gcacatttttggtgctagattgttctgcaacagtaactctaaagaacttcactattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCATTAAAAATTCAGCAGTTCAAT
||| | | ||| | | ||| || ||| ||| |||| ||| | ||| |||||||||| || || | || || ||||| ||||||||||| ||| ||||||| |||||||| | |||||||||||| || || |||||||| |||||||||||||| ||||||||| || || |
gacaaatacaccatgcagtcaactgcagaggaattgattctgcaaattcttgg-gctgaactgtaatgcaacagtattcttatgaaattctaccgtttcagCGCCTCCATTGTGGGTGTGTTGCTTCAAAGAACTCTTATGATCTACTTGACAGTGGAGGAGTTCATTGTGTCACTTGCATGAAAAATTCATTAGCCCAGT
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------gtgagatggtgacctatgctgtgaaatgtatgcacatttttggtgctagat--tgttctgcaacagtaactctaaagaacttcactattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCATTAAAAATTCAGCAGTTCAAT
|||| | || || |||| || | || | || | ||| | | ||| ||| ||||| || |||| ||| || ||||| ||||||||||||||| ||||||| |||||||| | |||||||||||| || || ||| ||||||||||||||||||| ||||||||||||| ||| |
gtgaggtggcgactcaagcctgcaaattctgctatgagatcctctgcagttgagtgtagtctgagcccgtggtgactttgtcactcatgcggtcgactgcagaggaatcgattctgcaaattcttgtgatgccacagtgttcttatgaaactctactgtttcagCGCCTCCATTGTGGATGTGTTGCTTCAAAGAACTCTTATGATCTACTTGACAGTGGAGGAATTCAATGTGTCACTTGCATGAAAAATTCAGCAGCTCAGT
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G04330.1 (Glycine max), 3'ss of exon 2
gtgagatggtgacctatgctgtgaaatgtatgcacatttttg-gtgctagattgttctgcaacag-taactctaaagaacttcact---attccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACT--TGATAGCGGTGGAGTTC--AATGTGTCACTTGCAT--TAAAAATTCAGCAGTTCAAT---------
| | |||| ||| | ||||| | || | | | | || | ||| || || ||| | | ||||| | |||| |||| | || | | || | || | |||| || ||| | ||| || | || | || ||
------------gtagagttaaaaaatatatacgtattttggtacactggtagagtatatagaagactagcataactctttttaccccaattttggtatttccatgttctatgttaagctt-aatgatcctatatgttttattatctgcagCGTCTCCATTGTGGATGCATTGCTTCTATGTCTCAGCTTGAATTATTAGATACTGGTGGT
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G32810.1 (Glycine max), 3'ss of exon 2
gtgagatggtgacctatgctgtgaaatgtatgcacatttttggtgc-tagattgttctgcaacagtaactctaaag--aacttcactattccagCGT-CTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCAT--TAAAAATTCAGCAGTTCAAT---------
|| | | || | || | | | | ||||| | | | || || ||| | | | | | || || |||| | || || |||| || | || | | | | || || | | | ||| | ||| || | || | || ||
gtagagttaaaaaagata-tatgtattttg-gtacattggtagagtatatataagactggcataactctttttaccccaattttggtatttccatgttctacattaaggtta-atgatcctatatgttttgtcttattatctgcagCGTCTCCATTGTGGATGCATTGCTTCTATGTCTCAGCTTGAATTATTAGATACTGGTGGT
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtgagatggtgacctatgctgtgaaatgtatgcacatttttggtgctagattgttctgcaacagtaac-tctaaagaacttcactattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCATTAAAAATTCAGCAGTTCAAT
| || || | | | || | ||| ||||| | | | | || | || | | | | || ||||||||||||||||||||||| |||||||| | | |||| ||||||||||| ||||| || | ||| | | ||||| | || ||||| | |||
gtcagttggtagtccagtaactcgtatcttgttccttcttcccaactcacatcactttttttct-tcaactcatgctattgttgaaaagtatgattcaattggtgtttccagCGTCTCCATTGTGGATGCATTGCTTCCAGGTCTCTGCTTGAGCTACTTGATAGTGGTGGCGTAAATTGTATTAACTGCATAAGAAGTTCAGGACCTCACCMapped 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|58607885|gb|CK035918.1|CK035918EST: AAAGAATCTGGCTGGAGGGACTGCTCATTTTGTGGGAAG CGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTTTAGCTT
genomic: AAAGAATCTGGCTGGAGGGACTGCTCATTTTGTGGGAAGgtgagatggt ... actattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATC--TA-CTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttggtgctagattgttctgcaacagtaactctaaagaacttcactattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCATTAAAAATTCAGCAGTTCAAT
cttcact CT-rich tract
taaagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatggtgacctatgctgtgaaatgtatgcacatttttggtgctagattgttctgcaacagtaactctaaagaacttcactattccagCGTCTCCATTGTGGATGTATTGCTTCGAAGAACTCCTTTGATCTACTTGATAGCGGTGGAGTTCAATGTGTCACTTGCATTAAAAATTCAGCAGTTCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG