Sequence
atgc intronic sequence ATGC exonic sequence...ttcctcttcagctgtcatggaagccgctttaagtcgcagagtataattacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07194.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G435034_T01 (Zea mays), 3'ss of exon 1
ttcctcttcagctgtcatggaagccgctttaagtcgcagagtataattacat--ctataaaaggtaa--tatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
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----gcatctacatccatgaaaactattagtgctcatatcatgtgtttacaatgctgagaaaagccagttagccacctttctcaaattatgaaacatttttcagATGTCTGAGCAATTCAACCAGGAGCTATCATTGTCTGGGAAAATTCCATCTGGCTTCTTCAATACTATGTTTGAGTTTTCTGGCAGCTGGCAGAAAGATG
upper sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G28780.1 (Glycine max), 3'ss of exon 2
-ttcctcttcagctgtcat---ggaagccgctttaagtcgcagagtataattacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
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agtggtaatgaattttctttttgtcaactgttttaagtattaagtaatgcatgcatcgtctccctttcat-tcactgtt--tgctccttttaaatgtttt-cagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
upper sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 1
-ttcctcttcagctgtcat---ggaagccgctttaagtcgcagagtataattacatc-tataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
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agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctccctttcactgactgtttgctc----cttttaaatgtttt-cagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
upper sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------------ttcctcttcagctgtcatggaagccgctttaagtcgcagagtataattacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
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gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttccttgtacattgttctagagagtaaatttcctt-catagcattttggatgccttagttattaacattt-tgttaacatttttcttatg-gtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
upper sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv12s0035g01040.t01 (Vitis vinifera), 3'ss of exon 2
ttcctcttcagctgtcatggaagccgctttaa-gtcgcagagtat-aattacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
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ttgttttacagttaattctaggacaatgttgatgctgtagcatattaaattcctctttcattgatttcgggtgcattgat--atttctttactttgctccagATGTCAGAGCAATTCAACCAGGAGATATCCTTGACTGGTAAAATTCCATCAGGCCTCTTCAATGCTATGTTTGAATTTTCAGGCTGTTGGCAGAAAGATGMapped 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|117247792|gb|CT848592.1|CT848592EST: ACAAAGGGGAGCGGACGCGGTTCCGGTCCGATGTCCTGTCATTTCAGCAG ATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCT
genomic: ACAAAGGGGAGCGGACGCGGTTCCGGTCCGATGTCCTGTCATTTCAGCAGgtacgtatca ... cattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCT
EST:
gi|58608642|gb|CK036675.1|CK036675EST: ACAAAGGGGAGCGGACGCGGTTCCGGTCCGATGTCCTGTCATTTCAGCAG ATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCT
genomic: ACAAAGGGGAGCGGACGCGGTTCCGGTCCGATGTCCTGTCATTTCAGCAGgtacgtatca ... cattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
tataaaaggtaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcctcttcagctgtcatggaagccgctttaagtcgcagagtataattacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG