Sequence
atgc intronic sequence ATGC exonic sequencegttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g10310.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029566_T02 (Zea mays), 3'ss of exon 5
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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-------------------------------------------------------------------------------------------tcaattatgggactagtataggtaactgtggtttatt-tcagtgacaattttctttatt--cactgtat----tatatcataataatt-gctggcttgttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttccc-ctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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--------------------------------------------------------------------------------------------------taggactagtataggaaactgtgctttgtt-ttagtgatagttttctttattcactaccttatgtcataatgcttgttggcttgttc-cttgttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAATGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G12100.1 (Glycine max), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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----------------------------------------------------------------------------------------------aatttcttctttgtatatagtttgttctaaatgagttatcttggtactgcattgtttttcatttattttatttaagcttaaaatc--ttagtttattg---gcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTTGATATTAACAATGCTGAAGATCACATCTTTGGACTTGTTGTAATGAACGATTGGAGTG
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G20850.1 (Glycine max), 3'ss of exon 2
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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----------------------------------------------------------------------------------------------------------gtatatagtt--atcatg-atactgcattatttttcttttgtttcaatttagattaaat-tattaaaa-----tcatagtttatt---tgcagGCTACTAATGTTGGACCGGGAAATGAATTGGGAAAACCTGTGGATATTAACTATGCTCAAGATCACATCTTTGGACTTGTTCTGCTGAATGACTGGAGTG
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G15210.1 (Glycine max), 3'ss of exon 2
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaatta--gttatagatattttcatttcccctggatcaaat-atatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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-------------------------------------------------------------------------------------------------------------------------gtatatatttatcatgatactgcattacttttcttttgtttcaatttagattaaattattaaaatcatagtttatttgcagGCTACTAATGTTGAACCGGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTGAAGATCACATCTTTGGACTTGTTCTGCTCAATGACTGGAGTG
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattc-ttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaat-atatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgag--gttaaacattgtttcattttcttctttgtatatagttatcatggtactg-cattatt-tttcatttgtttcattttagattaaattattaaaatcatagtttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG
upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0187g00340.t01 (Vitis vinifera), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaact-gttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
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gttagt---tgatatgcatttttatcc----tatttaagaattttaaactcatgattaattttagtatcaaat-tttgtcttat--gatgaatttatcgttactgcacca-gttgtcttgtcgt--gatatgtgttgtctctgattctattt-------gttaattatatg----------gcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCATATCTTTGGACTTGTGATCATGAATGACTGGAGTGMapped 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|4969133|gb|AU066037.1|AU066037EST: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTNAGATG GCAGCCATTGTTGGACCAGGGGATGAATTTGGGAAA
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATT-GGGAAA
EST:
gi|88324389|gb|CI566202.1|CI566202EST: CTCGACCTTATTTTGGTCCTTCTTCTAAGCTTGATTTTGAACTTGACATG GCAGCCATTGTTGGACCACGGAATGAATTGGAAAAAC-TATCGATATTAAT
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
EST:
gi|27548667|gb|CA766758.2|CA766758EST: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATG GCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
tcataac putative branch site (score: 2)
ttgctttc putative PPT
atcaaatatatcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG