Sequence
atgc intronic sequence ATGC exonic sequenceGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os10g29660.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G466938_T01 (Zea mays), 5'ss of exon 5
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
||||||||| |||| || || ||||| |||||||| |||| ||||||||||| ||||||||||| |||| | |||| | | | |||||||| || | ||| | || | || | | ||| | | ||| |||| || ||| || || || ||| | | || ||
GATTTCAAGGTCCAAAATATAGTTGGGTCATGTGACCTCAAGTTTCCTATTCGTCTGGAGGGCCTCGCTTTGGCCAGTGGCTTGTCTGCCACTgtaagtttatagcagctctttct---ttagttgtaaacgtgtttgttgtgt---cgttg---ttgatccccattgact------cattagcctgttgctctcttggtgtttgacag----------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G092916_T01 (Zea mays), 5'ss of exon 5
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
||||||||| |||| || || ||||| |||||||| |||| ||||||||||| ||||||||||| |||| | ||| | | | |||||||| || | | || | || | || | | |||| | ||||||| | | || | | | || |||| |
GATTTCAAGGTCCAAAATATAGTTGGGTCATGTGACCTCAAGTTTCCTATTCGTCTGGAGGGCCTCGCTTTGGCCAGTGGTTTGTCTGCCACTgtaagtt---tatagaagctctttctttagttgtaaacgtgtgtgttga-tccccattgacctgaagactcattagcctgttgctctcttggtgtttgacag------------------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G28780.1 (Glycine max), 5'ss of exon 7
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttg-aatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||| | || ||||| ||||||||| | | | | | | | || || || || || | || || || | || || |||||| || | |
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGTgtaagtgtgaaatgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgc--cctagta---atcagtcctatatatggtc----------------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagt-tgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| || ||||| ||||||||| ||| | | | || | | | | | | ||| | || || || | || || |||||| ||| | |
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgc--cctagta---atcagtcctacatatggtc----------------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
|||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| |||||||||| ||| || ||| | | | ||| | | ||| ||| | |||| || || | | | | | || | | | || |||
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagttattt--tttgggaaaataattcataggg------ttggattg-----gttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc-------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G25450.3 (Glycine max), 5'ss of exon 7
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
|||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| |||||||||| ||| |||||| | | || ||| | || || | || || || ||| | | | || | || |||
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagtt------ttaattttttgggaaaat--aaattggtccctggtgacttttatatcagaatattttgttttcacaatcaatgtttggctatc-----ctgatgtttagg-------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgatt--acttacttttttacattgtctcagaatgcatcctttgaatttccat-tgaaactgatgccagttg--tctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
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GATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGTgtgagtgatcttaacttatacattta-gtagtcaaggaccgacttttagagataaaaacgttgtgctgatggccattacctctctctcatattggcgtgtggttag-------------------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgt---ctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
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GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagt-gatctcaagcattgtgatcatatatacttgtaacatgggtgtt-aatcggtctgatgattcatacctctctcatcattgatgccag------------------------------------------------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 5'ss of exon 6
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
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GATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGTgtgagc--atctctggcttgcttacatgatct----acgggaaatatgaacgcttgtgtgaaatgtttcgacacga-tgatatttat--gcgcccaaacccactgaatg-----------------------------------------------Mapped 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|8324452|gb|AU091604.1|AU091604EST: TTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT TATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAG
genomic: TTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgat ... taatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG