Sequence
atgc intronic sequence ATGC exonic sequencegtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11550.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11550.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 6
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
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----------------------------------------------------------------------------ggaatagtggcttcgcttggcctggctaaactttgtattgccatatggttcc-tttaagctgcactggt-------tggcatgactaatctt------ttttttccctgtgcagTACTTTGATTTGCTCAACATATTTGACCTCAATGGCCTTCCATCAGAAGAAAATCCTTACCTCTTCAATGGCGATTTTGTGGACCGAGGATCTTTCTCCG
upper sequence: LOC_Os05g11550.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 7
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG-
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---------------------------------------------------------------------------------------gaaggtcctccatcattgcagggcatttgtatttttgtatt-tttatctttaatttttaactttgcaaattcatt---attatttgttttctgtcttctgcagtACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCCTTTTCATT
upper sequence: LOC_Os05g11550.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 7
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttt-tccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
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-------------------------------------------------------------------------------------cttcttttatcctgttgcatcattttgcttggcttttgaatttttttctttaatttt--taaccttgcaatttcattagtatt----tgttttccatcttctgcagTACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCTTTTTCAT
upper sequence: LOC_Os05g11550.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
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----------------------------------------------------------------------------gtactagaatttctattttagagggggtgttttgtgttcgctgtctagt---actcattgcattcggcttgtcagagtatttaacttggattctggaa-------ccaatgcagTACTATGATTTACTCAACATTTTCAAGCTGAATGGTCTTCCTTCAAAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCTTTTTCGG
upper sequence: LOC_Os05g11550.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S87_139V6.2 (Physcomitrella patens), 3'ss of exon 7
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
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---------------------------------------------------------------------gtactataaaat--tctttgtaggggca-atgct----ttgtattttccgtgtg--ttacttcatgacttggtgtttgacatgatttctaactaggaggatgatggaattgac----gcagTACTATGACTTGCTGAACATTTTCAAGCTTAATGGTCTCCCCTCGGAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCATTTTCGGMapped 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|33684365|gb|CF312604.1|CF312604EST: ACGTTCCTGATGGAAGTCATTTTACGGTTTGTGGTGATGTGCATGGTCAG TATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAG
genomic: ACGTTCCTGATGGAAGTCATTTTACGGTTTGTGGTGATGTGCATGGTCAGgtatttaaat ... tccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAG
EST:
gi|29676952|gb|CB673227.1|CB673227EST: ACGTTCCTGATGGAAGTCATTTTACGGTTTGTGGTGATGTGCATGGTCAG TATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAG
genomic: ACGTTCCTGATGGAAGTCATTTTACGGTTTGTGGTGATGTGCATGGTCAGgtatttaaat ... tccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAG
EST:
gi|33793725|gb|CF322745.1|CF322745EST: CGTTCCTGATGGAAGT-ATTTTACGGTTTG-GGNTGATGTGCATGGTCAG TATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAG
genomic: CGTTCCTGATGGAAGTCATTTTACGGTTTGTGG-TGATGTGCATGGTCAGgtatttaaat ... tccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
tatttttttccact CT-rich tract
attggaattgtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttaaattttttgaatgcattgcttttgtttttttcctagtgcttctgggtgtccccttcttttttgaaatggaaaatgatattggtaatttcacatgctaaaattttagctgtcatttgatttagtttattacatattgatatactgacagcctgattggaattgtaatatttttttccactgcagTATTTTGACTTGCTCAATATATTTAAGCTCAATGGGCTTCCCTCGGAAGAGAATCCTTACCTCTTCAATGGAGACTTTGTAGACAGAGGATCTTTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT