Sequence
atgc intronic sequence ATGC exonic sequencegtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 14
gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC---
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gtaagatattgtatcgtc-aaatgattattatcttgtttctttt-tccttttacccaccttgtgatgcatgg----------cgttataa-acaaa---atgactatgatatgtgctttt-tagAGAGATGTTGTTGCTTCTTATCTAGAAGGTGGAAAGCCTGTGGATGA---AGGTGTCGAAGATGCTTTTGAGCTGCTTCACGAGGTCAATGAGCGAGTGAGAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 14
gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
||||| |||||||| || ||||| | ||||| | |||||||| | |||| | |||| | || || || | || ||||||| | | ||||||||| | ||||| |||||||||||| |||||| |||||||| || |||||||||||||||||||||||||||||||||||| | ||||||||||||
gtaagatattgtatcctc-aaatgattattatctagtttctttttccttcttttacccacctccttgtgatgatggggattataacacaaaacgag------------atttgtgctt-tgcagAGAGATATTGTTGCTTCTTATCTAGAAGGTGGAAAGCCTGTGGACGAAGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGATCAATGAGCGAGTGA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 14
-------------------------gtaagttattg-tattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
| |||| | | || || | | | || || | | || | | | | | ||| || ||||| | || | | | || | | | || | | ||| | ||||| |||| || || |||| ||||| |||||| ||||| ||||| |||||||||||||||||||| | ||||| | ||||| || ||
gtgaggactctcatgaacttcatcttttccttatagatgttggcttgctttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacat---tttgacttccactattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
-----------------------gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttt---tttacca-tggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
| | || | | | | | || || | || ||| || | | | | | || |||| | | |||| | || ||| | || ||| || || | ||| | ||||||||||| || ||| |||| ||||| ||||| |||||| |||| ||||||||||| |||||||| |||||||| | ||||| || ||
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 14
------------------------------gta-agttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatg--tgttattgcgtgaa--------agttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
|| |||| ||| || | | | ||| || | | | | | | || || | || ||||| | || | | | || || | || || | ||| | ||||| |||| || || |||| ||||| |||||| ||||| ||||| |||||||||||||||||||| | ||||| | ||||| || ||
gtgaggattttcgtgaacttcatcttttccttatagttgttggcttgctttgaagaacatcccaccccctccccccaacacacacacaatttctgctgaatgtatattttgtagatctttactggtagtgcccttgaaacatatt---gacttccattattgcagCGTGATGTTGTTGTATCACATTTAGATAGTGGAAGACCTGTAGATGATGAAGGTGTTGAAGATGCTTTTGAGCTCTTACATGAAATGAATGAACGTGTCA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
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--------gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttacta----gtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCAMapped 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|58660118|gb|CK048798.1|CK048798EST: ACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC AGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAA
genomic: ACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAACgtaagttatt ... gttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAA
EST:
gi|29630380|gb|CB635389.1|CB635389EST: ACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC AGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAA
genomic: ACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAACgtaagttatt ... gttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
tgttcct CT-rich tract
ttatgtttgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT