Sequence
atgc intronic sequence ATGC exonic sequencegtaagcacctagatttatcccattcattgctgttgcctcgtgttcctcatcatttgtgtttatgtattaaaagtaataacatcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 6
gtaagcacctagatttatcccattcattgctgttgcctcgtgttcctcatcatttgtgtttatgtattaaaagtaataaca-tcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
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gtaagtatct---tccattctttttaatggtat---cttttgtcactcat-gtatcagcttctagactaaacgagtcaacaatctcaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCAATTCTTGAGAAGCTCCATTCTAAAGG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 6
gtaagcacctagatttatcccattcattgctgt--tgcctcgtgttcctcatcatttgtgtttatgtattaaaagtaataac-atcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
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--------gtaagtatcttccattcttttttatgatatcttttgtcactcatca-----gcttttagactaaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------gtaagcacctagatttatcccattcattgctgt--tgcctcgtgttcctcatcatttgtgtttatgtattaaaagtaataaca-tcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
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ggtatgttgtttatggtatttcagctgtatttaattcgatggggcaggca--taagtatcttccattcttttttatggtatcttttgtcactcat-gtatcagCTTCTAGACTAAACGAGTCAACAATCTCAAACAGGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCAATTCTTGAGAAGCTCCATTC------
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 6
gtaagcacctagatttatcccattcattgctgttgcctcgtgttcctca--------tcatttg---tgtttatgtattaaaagtaataacatcatta------acagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
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gtaag-atttgtaccc-tcccttttgttagtataggttcacttttaatagctgcaatttatttaaactcttcctatataagccccattaacattttagttctggacagAATGTCACCAAATATGGTTGCGTGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcacctagatttatcccattcattgctgttgcctcgtgttc-ctcat-------catttgtgtttatgtattaaaagtaataacatcat-taacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
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gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGGMapped 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|66915500|gb|CX102348.1|CX102348EST: GATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC GATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCT
genomic: GATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGACgtaagcacct ... tcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcgtgttcctcatcatttgtgtttatgtattaaaagtaataacatcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
taataac putative branch site (score: 1)
tttatgtattaaaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcacctagatttatcccattcattgctgttgcctcgtgttcctcatcatttgtgtttatgtattaaaagtaataacatcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC