Sequence
atgc intronic sequence ATGC exonic sequencegtatgccgtgtattagcttgatgctaagcttttttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g37580.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G057475_T03 (Zea mays), 3'ss of exon 6
gtatgccgtgtattagcttgatgctaagctttt-----ttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcccactatctatttctggggcactaaga--gaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
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gtatgcagcatataatttctatgctaactatttgaaaacaacagctgagaacacagaccaccttcctcagagattgctccatcactttctct-tttgccgcagtaaaatttaattgacaactgacaagcctgaaaatgatatatgaactgcagGTCTGGTGGCTGATGTTGATATTGAATCGGAGAAGTATAGGTGGATGGGAAGTGCTCGCCTTGAATTTTAT
upper sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
gtatgccgtgtattagcttgatgctaagcttttttctctcttaaactacacgtctatacccccataacactgactgtcactctcag-agcttgttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
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gta-attataaattactgtcaccatagtcgtgttttggaaacgag-tgaatgtgaaaaagcatctaa-----gttacttgtgtcagcatctggttctggccatgatattcgccgtaaca-tatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
upper sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G07340.1 (Glycine max), 3'ss of exon 6
----------------------------------gtatgccgtgtattagc---ttgatgctaagctttt----ttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
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gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcgcaattttttctttctcttcttgatt-tatccagacttaggtgattcttagt-tctgaccatgcaattgacttgacatattatatgatatccattggaggt-attattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
upper sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G21534.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgccgtgtattagcttgatgctaagcttttttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcc-cactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
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-------gtatgccag-taaattcta--cttctttttgctatgtccagagttcagaaagttatttgcaaatgaaagtaatacat-gagcttgctgaacgtactctttgtt------gtatt--gattagtccatttat----ttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
upper sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0181g00250.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------gtatgccgtgtatt--agcttgatgctaagct---tttttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcccactatctat--ttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
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gtatgaccaaaatttccaccacttgtttatgccatactcttggaactgcaagtgactgttgaactggatttttaagacaagctttctaagaatatgcctctggatttactagaataagctttctagtggatttgtttgattttgatagctctactttgccttactgacagaattttagtattccagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAATATAGGTGGATGGGAAGTGCTCGTTTAGATTTCTACMapped 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|218479329|gb|FG969597.1|FG969597EST: TGTTGTGCAGGGAAAGACAA-GTTTTTTAGTGTCTTGATGCTTACTTGGG GTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCA
genomic: TGTTGTGCAGGGAAAGACAAGGTTTTTTAGTGTCTTGATGCTTACTTGGGgtatgccgtg ... tgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
tatctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccgtgtattagcttgatgctaagcttttttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA