Sequence
atgc intronic sequence ATGC exonic sequence...ggccagaaatgagtaacataacaagtcgtatatgcctgtctattgcaatatgttactgattcctgtaacatttagtcacttttactatttaattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g39570.6 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 6
----ggccagaaatgagtaacataacaagtcgtatatgcctgtctattgcaatatgttactgattcctgtaacatttagtcacttttactatttaattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT
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agttgttcagactttcatcagatg-catttgatacagtattacagtctgcacactagtcctggctcgtataacatgtagt---tttgactttggaactgtccagGGTGATGTTTATCCTGTGGAATCTTACGAGAGCTCAGCTA---ACCAAGTACTTGATGCTCACTGGGGTGTTCTGGATGATGATGAT
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 7
--ggccagaaatgagt--aacataacaagtcgtatatgcctgtctattgcaatatgttactgattcctgtaacatttagtcacttttactatttaattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT
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ttgttcagatttccatctggcgcatttgatacaatattacagtcta---cacactattcctggctcttataacatgtt-ttgttttgactttggcactgtccagGGTGATGTTTATCCTGTGGAATCTTACGAGAGCTTATCAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 6
ggccagaaatgagtaacataacaagtcgt--atatgcctgtctattgcaatatgttactgattcctgtaacatttagtcacttttactatttaattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT
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gtttgatattttccctcccttctgttctttgatttatttgctcattagtaaattcaaatatagtctgacctcttcttttgacatgtttgcttg--tgtgaagGGAGATGTTTATCCTATAGAGCCACCAGATGGTTTTACAGTCAATCAAGTACTTGATGCTCACTGGGGTGTCCTCAATGAAGAAGATMapped 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|58601913|gb|CK012441.1|CK012441EST: CTGTAAATAAGACAGTCAATGGAAGTTTTGATCAACCATCCAATGCTGGG GGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTA
genomic: CTGTAAATAAGACAGTCAATGGAAGTTTTGATCAACCATCCAATGCTGGGgtatgtttct ... aattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTA
EST:
gi|33682200|gb|CF310439.1|CF310439EST: CTGTAAATAAGACAGTCAATGGAAGTTTTGATCAACCATCCAATGCTGGG GGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTA
genomic: CTGTAAATAAGACAGTCAATGGAAGTTTTGATCAACCATCCAATGCTGGGgtatgtttct ... aattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatgttactgattcctgtaacatttagtcacttttactatttaattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT
ttttactatttaattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggccagaaatgagtaacataacaagtcgtatatgcctgtctattgcaatatgttactgattcctgtaacatttagtcacttttactatttaattgttcagGGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA