Sequence
atgc intronic sequence ATGC exonic sequencegtaagttatgtctatgaagcatcttaatatagaaagatgacaatgcttatataactaaatttattttttggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g37430.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G038667_T02 (Zea mays), 3'ss of exon 7
gtaagtt-atgtctatgaagca--tcttaatatagaaagatgacaatgcttatataactaaatttattttttggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
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gtaagttgacagctattgaatagatcgtattatacacaaccagcaaacttca---aaataaactctgttttt-----tcagCGCTGTGGAATTCTTGAAACAAGTCCTTGGAACTTACAGTTTAAGATATATGAAGGCTTCTCGTATGCTTGGTGACCAATTAGCACTTGCATGGGTTGTC
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G350001_T01 (Zea mays), 3'ss of exon 10
gtaagtt-atgtctatgaagcatct--taatatagaaagatgacaatgcttatataactaaatttattttttggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
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gtaagttgacagctattgaatatatcgtattatacacagccagcaaacttca---aattaaactctgttttt----ttcagAGCTGTGGAATTCTTGAAACAGGTCCTTGGAACTTACAGCTTAAGATATATTAAGGCTTCCCGTATGCTTGGTGACCAATTAGCACTTGCATGGGTCGTC
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143688_T01 (Zea mays), 3'ss of exon 4
gtaagtt-atgtctatgaagcatct--taatatagaaagatgacaatgcttatataactaaatttattttttggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
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gtaagttgatagctattgaatatatcatattatacacagccagtaaatttcaaatta--aaatctgtttttt----ttcagAGCTGCGGAATTCTTGAAACAAGTCCTTAAAGCTTACAGCTTAAGATATATTAAGGCTGCCCGTATGCTTGGTGACCAATTAGCACTTGCATGGGTTGTC
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 3
---------------gtaagttatgtctatgaag----catcttaatatagaaagatgacaatgcttatataactaaatttattttttggcttt---tagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
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tgcgtgttctattttgtggattctgtttctccaatgatcatctgaaaattaaatccttttcattttccattttttgaatttaatttgagaatctatgcagGGCAAAGCTTTTCCTACAAGAGGTCTTGAAAGTTTACAGCACAAAATATAGAAATGCTTCCCGCATGCTGGGTGATCAATTAGCTCTTGCTTGGGTTGTGMapped 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|29671600|gb|CB667875.1|CB667875EST: TTGAATTCTGGATTTGTAGCAGTAAGAGGAACCAGGGATGGCATTTTTAA GGCTATTGAATTCTTCANAGAAGTCCTTGAGGCATACTACTTGAAGTATAT
genomic: TTGAATTCTGGATTTGTAGCAGTAAGAGGAACCAGGGATGGCATTTTTAAgtaagttatg ... tggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatagaaagatgacaatgcttatataactaaatttattttttggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
aactaaa putative branch site (score: 2)
tttatttttt CT-rich tract
ttatataactaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttatgtctatgaagcatcttaatatagaaagatgacaatgcttatataactaaatttattttttggcttttagGGCTATTGAATTCTTCAAAGAAGTCCTTGAGGCATACTACTTGAAGTATATGGAGGCTTCCCGCATGCTTGGTGATCAATTAGCACTGGCATGGGTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG