Sequence
atgc intronic sequence ATGC exonic sequence...acaggattgtatgttgacatgttccagattgttcaactggaccatacagttccagaagttctagtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------acaggattgtatgttgacatgttccagattgtt-caactggaccatacagttccagaagttcta----gtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
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gtaattttcctgtacattgcagttcatataatgttcagaaaggtactgcagagaaaaaagatccattccatttctagtgtaggatctttttgataaaattggatatttttgctgccaagatgctaaaatgtaatgaatacacagGGTCTAAGACAGGAGGTTATTGTGGACCTTGTGGATCAATGTCGTTCTTACAAGCAGAGGGTGGTACAGCTTGTCAACTCAACCAC
upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 6
--------------------------------acaggattgtatgttgacatgttccagattgttcaactggaccatacagttccagaagttctagtcatccctggatttctaa---atagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
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gtaagttgttcaatccaaactttcaaattatgatgtaaatgaataaaaatattttgtgaagcttaaggtttttatcaacagaactactgattctattgaatatatgacatttcatttatgaccttctattttcagGGGCTTCAGCAGGAAGTTATTGTTGATTTAGTGGAGCAATGTCGAACATACAAGCAGAGAGTGGTGCACCTTGTTAATTCAACTTC
upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 6
---acaggattgtatgttgacatgttccagat---tgtt--caactggaccatacagttccagaagttctagtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
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gtaacacgatttagttgcagagtgtttgagctacctgtttacaagtgtaggctatagcccaaaatatactaaataatgatcattcttctcgtttttggatttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC
upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 6
-acaggattgtatgttgac--atgttccagattgttca-actggaccatacagttccagaagttctagtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
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tatgcatttgtgtcatccttgaggtttttttttgcacatattagatttctttagttcagtctctgtgttcatgttgggttatttttgtcctaattaac----agGGGCTCAGGCAGGAGGTTATCATGGACTTGGTAGATCAGTGTCGGACATACAAGCAAAGAGTGGTCCACCTTGTCAACTCAACTGCMapped 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|26456448|gb|CA828031.1|CA828031EST: TGGATGTTCTTTCAGAGATGTTAAATGCTATCGATCCTGGTAACAGAGAG GGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATAC
genomic: TGGATGTTCTTTCAGAGATGTTAAATGCTATCGATCCTGGTAACAGAGAGgtattttcta ... caacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATAC
EST:
gi|78118618|gb|DV537002.1|DV537002EST: TGGATGTTCTTTCAGAGATGTTAAATGCTATCGATCCTGGTAACAGAGAG GGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCTATGTCGTTCATAT
genomic: TGGATGTTCTTTCAGAGATGTTAAATGCTATCGATCCTGGTAACAGAGAGgtattttcta ... caacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATA-
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagttccagaagttctagtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
ttctaaa putative branch site (score: 2)
atttctaaatagta 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
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acaggattgtatgttgacatgttccagattgttcaactggaccatacagttccagaagttctagtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT