Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtcttgacatattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47290.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G427620_T01 (Zea mays), 3'ss of exon 5
------gtatgagtcttgacat-attgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
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cttcttccatatgttctggtatgaatggggtttatttgccgattctgtctcagct--------ttactttgtggccaatatatctgattgttt-gctggatt--tgtccagGCTAATTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACA
upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 10
gtatgagtcttgac-atattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
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gtacgagtggggcctattttgttgtttcctttgtgtctctgctttactttgtggcacaaattatttgctcactttcttttgtg-------------------cagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG
upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G544990_T01 (Zea mays), 3'ss of exon 9
gtatgagtcttgacatattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
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--------------gtatgaatggggtttatttgccgattctgt-ctcatc----tttactttgtggccaaattatctgattgttt-gctggatt--tgtccagGCTAATTTTCTTCAAGCTGTTGTTGACTACAAGAAGAAGATTGGATTCAACG
upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 9
gtatgagtcttgacatattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
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--------------gtatgaatggggtttatttgccgattctgtcttagct-----ttactttgtggccaaattatctgattgttt-gctggatt--tgtccagGCTAATTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG
upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 10
gtatgagtcttgacatattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
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gtatgaat---ggggtttatttgccgattctgtgtctcagct--------------ttactttgtggccaaattatctgattgttt-gctggatt--tgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGMapped 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|29637953|gb|CB642962.1|CB642962EST: GTTACCAAACTCTTCTTAATACTGACATGAAGAGAGAACTTGACCATTTG GCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAAT
genomic: GTTACCAAACTCTTCTTAATACTGACATGAAGAGAGAACTTGACCATTTGgtatgagtct ... tgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAAT
EST:
gi|88306647|gb|CI671406.1|CI671406EST: GTTACCAAACTCTTCTTAATACTGACATGAAGAGAGAACTTGACCATTTG GCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAAT
genomic: GTTACCAAACTCTTCTTAATACTGACATGAAGAGAGAACTTGACCATTTGgtatgagtct ... tgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
attttgatttatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtcttgacatattgttactgttcctctgtttctgttacacttactaccactcactttatctccattttgatttatcattttgccgtgttgtcatccagGCTAGTTTTCTTCAAGCTGCAGTTGACTACAAGAAGAAGATTGGATTTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG