Sequence
atgc intronic sequence ATGC exonic sequence...tttattttgtttaatgttacaaagaaatgtttgtaggcatatgtattgcattcatcatttgatagcatcaattaacatccttgatttctttctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACTGGAGAAGAGATTAAGAACAAGAGACAGCTGAGCCAGTATCTGAAGGCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g42550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g42550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G022365_T01 (Zea mays), 3'ss of exon 1
-tttattttgtttaatgttacaaagaaatgtttgtaggcatatgtattgcattcatcatttgatagcatcaattaacatccttgatttctttctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACTGGAGAAGAGATTAAGAACAAGAGACAGCTGAGCCAGTATCTGAAGGCAC
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agagctgttactagacactcatttctttcattagtgaatgtatgttttatgggga-catctgattgcatgaactaatattccttctttttcaatgttacagTTTACTCCCCAGAGAGGGGGAAGATCCGAGATTGTTTTTGTTTCGCCAACTGGCGAGGAAATTAAGAACAAGAGGCAACTAAGCCAATACCTAAAGGCAC
upper sequence: LOC_Os12g42550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G476933_T01 (Zea mays), 3'ss of exon 1
tttattttgtttaatgttacaaagaaatgtttgtaggca-tatgtattgcattcat-catttgatagcatcaattaacatccttgatttctttctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACTGGAGAAGAGATTAAGAACAAGAGACAGCTGAGCCAGTATCTGAAGGCAC
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aaagagctgttagtaggcacacatttctttcattagttaatgtgtattttatggggatatctgattggg--aactaatatacattcctttttaatgttacagTTTACTCCCTTGAGAGGGGGGAGATCTGAGATTGTTTTTGTTTCACCAACTGGTGAGGAAATTAACAACAAGAGGCAATTACTTCAGTACCTAAAGGCACMapped 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|58686077|gb|CK074764.1|CK074764EST: TGGACGAAGAAG TTTACTCCCCAGAGAGGGGGGACATTTGAGATTGTTTTTGTTTCACCAACT
genomic: TGGACGAAGAAGgttcgagacg ... tctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACT
EST:
gi|33684770|gb|CF313009.1|CF313009EST: GGTGGTGTCCGTGGAGATGCCGGCGCCGGAGGGGTGGACGAAGAAG TTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACT
genomic: GGTGGTGTCCGTGGAGATGCCGGCGCCGGAGGGGTGGACGAAGAAGgttcgagacg ... tctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcattcatcatttgatagcatcaattaacatccttgatttctttctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACTGGAGAAGAGATTAAGAACAAGAGACAGCTGAGCCAGTATCTGAAGGCAC
tccttgatttctttct CT-rich tract
atcaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttattttgtttaatgttacaaagaaatgtttgtaggcatatgtattgcattcatcatttgatagcatcaattaacatccttgatttctttctattgtagTTTACTCCCCAGAGAGGGGGGAGATTTGAGATTGTTTTTGTTTCACCAACTGGAGAAGAGATTAAGAACAAGAGACAGCTGAGCCAGTATCTGAAGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - aaagaaa
- - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - -tatgtat
- - - - - - - - - - - - - - - - - - - - - - - tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tcatttg