BLAST

1. Conceptual translation of Alzheimers susceptibility protein L43964
   1. TBLASTN vs. dbEST
   2. Goal: Identify cDNA clones for potential homologs in model organisms
      • Result - mouse and drosophila found
      • Find alignment for AA602396
      • Frames are adjacent to each other and indicate a reading frame error in the EST seq
2. 3' end of CBFB transcription factor L20298 contains an Alu element
   BLASTN vs nr
   • Lots of genomic hits
   • No Alu warnings

   BLASTN vs Alu

   • Alu J warning
3. EDG1 receptor NM_001400

Locus Link

Example of locus link file

Unigene

1. U95089 EGFR truncated protein
   1. notice that most of the information is about EGFR.
   2. You must be aware of the differences that may be present with your accession number
2. M15169 - cluster id retired
   1. Notice multiple copies of accession number.
   2. Usually indicates different coding regions of same gene
3. Examples of data format
   1. Rn.data
   2. Rn.lib.info
   3. Rn.seq.uniq

ORF Find

M15169 has no listed cds

Promoter Prediction

>gi|35886|emb|V00574.1|HSRAS1 Human germ line gene homologous to bladder carcinoma oncogene T24 (Gene code c-Ha-ras-1) with four exons
GGATCCCAGCCTTTCCCCAGCCCGTAGCCCCGGGACCTCCGCGGTGGGCGGCGCCGCGCTGCCGGCGCAG
GGAGGGCCTCTGGTGCACCGGCACCGCTGAGTCGGGTTCTCTCGCCGGCCTGTTCCCGGGAGAGCCCGGG
GCCCTGCTCGGAGATGCCGCCCCGGGCCCCCAGACACCGGCTCCCTGGCCTTCCTCGAGCAACCCCGAGC
TCGGCTCCGGTCTCCAGCCAAGCCCAACCCCGAGAGGCCGCGGCCCTACTGGCTCCGCCTCCCGCGTTGC
TCCCGGAAGCCCCGCCCGACCGCGGCTCCTGACAGACGGGCCGCTCAGCCAACCGGGGTGGGGCGGGGCC
CGATGGCGCGCAGCCAATGGTAGGCCGCGCCTGGCAGACGGACGGGCGCGGGGCGGGGCGTGCGCAGGCC
CGCCCGAGTCTCCGCCGCCCGTGCCCTGCGCCCGCAACCCGAGCCGCACCCGCCGCGGACGGAGCCCATG
CGCGGGGCGAACCGCGCGCCCCCGCCCCCGCCCCGCCCCGGCCTCGGCCCCGGCCCTGGCCCCGGGGGCA
GTCGCGCCTGTGAACGGTGAGTGCGGGCAGGGATCGGCCGGGCCGCGCGCCCTCCTCGCCCCCAGGCGGC
AGCAATACGCGCGGCGCGGGCCGGGGGCGCGGGGCCGGCGGGCGTAAGCGGCGGCGGCGGCGGCGGGTGG
GTGGGGCCGGGCGGGGCCCGCGGGCACAGGTGAGCGGGCGTCGGGGGCTGCGGCGGGCGGGGGCCCCTTC
CTCCCTGGGGCCTGCGGGAATCCGGGCCCCACCCGTGGCCTCGCGCTGGGCACGGTCCCCACGCCGGCGT
ACCCGGGAGCCTCGGGCCCGGCGCCCTCACACCCGGGGGCGTCTGGGAGGAGGCGGCCGCGGCCACGGCA
CGCCCGGGCACCCCCGATTCAGCATCACAGGTCGCGGACCAGGCCGGGGGCCTCAGCCCCAGTGCCTTTT
CCCTCTCCGGGTCTCCCGCGCCGCTTCTCGGCCCCTTCCTGTCGCTCAGTCCCTGCTTCCCAGGAGCTCC
TCTGTCTTCTCCAGCTTTCTGTGGCTGAAAGATGCCCCCGGTTCCCCGCCGGGGGTGCGGGGCGCTGCCC
GGGTCTGCCCTCCCCTCGGCGGCGCCTAGTACGCAGTAGGCGCTCAGCAAATACTTGTCGGAGGCACCAG
CGCCGCGGGGCCTGCAGGCTGGCACTAGCCTGCCCGGGCACGCCGTGGCGCGCTCCGCCGTGGCCAGACC
TGTTCTGGAGGACGGTAACCTCAGCCCTCGGGCGCCTCCCTTTAGCCTTTCTGCCGACCCAGCAGCTTCT
AATTTGGGTGCGTGGTTGAGAGCGCTCAGCTGTCAGCCCTGCCTTTGAGGGCTGGGTCCCTTTTCCCATC
ACTGGGTCATTAAGAGCAAGTGGGGGCGAGGCGACAGCCCTCCCGCACGCTGGGTTGCAGCTGCACAGGT
AGGCACGCTGCAGTCCTTGCTGCCTGGCGTTGGGGCCCAGGGACCGCTGTGGGTTTGCCCTTCAGATGGC
CCTGCCAGCAGCTGCCCTGTGGGGCCTGGGGCTGGGCCTGGGCCTGGCTGAGCAGGGCCCTCCTTGGCAG
GTGGGGCAGGAGACCCTGTAGGAGGACCCCGGGCCGCAGGCCCCTGAGGAGCGATGACGGAATATAAGCT
GGTGGTGGTGGGCGCCGGCGGTGTGGGCAAGAGTGCGCTGACCATCCAGCTGATCCAGAACCATTTTGTG
GACGAATACGACCCCACTATAGAGGTGAGCCTGGCGCCACCGTCCAGGTGCCAGCAGCTGCTGCGGGCGA
GCCCAGGACACAGCCAGGATAGGGCTGGCTGCAGCCCCTGGTCCCCTGCATGGTGCTGTGGCCCTGTCTC
CTGCTTCCTCTAGAGGAGGGGAGTCCCTCGTCTCAGCACCCCAGGAGAGGAGGGGGCATGAGGGGCATGA
GAGGTACCAGGGAGAGGCTGGCTGTGTGAACTCCCCCCACGGAAGGTCCTGAGGGGGTCCCTGAGCCCTG
TCCTCCTGCAGGATTCCTACCGGAAGCAGGTGGTCATTGATGGGGAGACGTGCCTGTTGGACATCCTGGA
TACCGCCGGCCAGGAGGAGTACAGCGCCATGCGGGACCAGTACATGCGCACCGGGGAGGGCTTCCTGTGT
GTGTTTGCCATCAACAACACCAAGTCTTTTGAGGACATCCACCAGTACAGGTGAACCCCGTGAGGCTGGC
CCGGGAGCCCACGCCGCACAGGTGGGGCCAGGCCGGCTGCGTCCAGGCAGGGGCCTCCTGTCCTCTCTGC
GCATGTCCTGGATGCCGCTGCGCCTGCAGCCCCCGTAGCCAGCTCTCGCTTTCCACCTCTCAGGGAGCAG
ATCAAACGGGTGAAGGACTCGGATGACGTGCCCATGGTGCTGGTGGGGAACAAGTGTGACCTGGCTGCAC
GCACTGTGGAATCTCGGCAGGCTCAGGACCTCGCCCGAAGCTACGGCATCCCCTACATCGAGACCTCGGC
CAAGACCCGGCAGGTGAGGCAGCTCTCCACCCCACAGCTAGCCAGGGACCCGCCCCGCCCCGCCCCAGCC
AGGGAGCAGCACTCACTGACCCTCTCCCTTGACACAGGGCAGCCGCTCTGGCTCTAGCTCCAGCTCCGGG
ACCCTCTGGGACCCCCCGGGACCCATGTGACCCAGCGGCCCCTCGCGCTGTAAGTCTCCCGGGACGGCAG
GGCAGTGAGGGAGGCGAGGGCCGGGGTCTGGGCTCACGCCCTGCAGTCCTGGGCCGACACAGCTCCGGGG
AAGGCGGAGGTCCTTGGGGAGAGCTGCCCTGAGCCAGGCCGGAGCGGTGACCCTGGGGCCCGGCCCCTCT
TGTCCCCAGAGTGTCCCACGGGCACCTGTTGGTTCTGAGTCTTAGTGGGGCTACTGGGGACACGGGCCGT
AGCTGAGTCGAGAGCTGGGTGCAGGGTGGTCAAACCCTGGCCAGACCTGGAGTTCAGGAGGGCCCCGGGC
CACCCTGACCTTTGAGGGGCTGCTGTAGCATGATGCGGGTGGCCCTGGGCACTTCGAGATGGCCAGAGTC
CAGCTTCCCGTGTGTGTGGTGGGCCTGGGGAAGTGGCTGGTGGAGTCGGGAGCTTCGGGCCAGGCAAGGC
TTGATCCCACAGCAGGGAGCCCCTCACCCAGGCAGGCGGCCACAGGCCGGTCCCTCCTGATCCCATCCCT
CCTTTCCCAGGGAGTGGAGGATGCCTTCTACACGTTGGTGCGTGAGATCCGGCAGCACAAGCTGCGGAAG
CTGAACCCTCCTGATGAGAGTGGCCCCGGCTGCATGAGCTGCAAGTGTGTGCTCTCCTGACGCAGGTGAG
GGGGACTCCCAGGGCGGCCGCCACGCCCACCGGATGACCCCGGCTCCCCGCCCCTGCCGGTCTCCTGGCC
TGCGGTCAGCAGCCTCCCTTGTGCCCCGCCCAGCACAAGCTCAGGACATGGAGGTGCCGGATGCAGGAAG
GAGGTGCAGACGGAAGGAGGAGGAAGGAAGGACGGAAGCAAGGAAGGAAGGAAGGGCTGCTGGAGCCCAG
TCACCCCGGGACCGTGGGCCGAGGTGACTGCAGACCCTCCCAGGGAGGCTGTGCACAGACTGTCTTGAAC
ATCCCAAATGCCACCGGAACCCCAGCCCTTAGCTCCCCTCCCAGGCCTCTGTGGGCCCTTGTCGGGCACA
GATGGGATCACAGTAAATTATTGGATGGTCTTGATCTTGGTTTTCGGCTGAGGGTGGGACACGGTGCGCG
TGTGGCCTGGCATGAGGTATGTCGGAACCTCAGGCCTGTCCAGCCCTGGGCTCTCCATAGCCTTTGGGAG
GGGGAGGTTGGGAGAGGCCGGTCAGGGGTCTGGGCTGTGGTGCTCTCTCCTCCCGCCTGCCCCAGTGTCC
ACGGCTTCTGGCAGAGAGCTCTGGACAAGCAGGCAGATCATAAGGACAGAGAGCTTACTGTGCTTCTACC
AACTAGGAGGGCGTCCTGGTCCTCCAGAGGGAGGTGGTTTCAGGGGTTGGGGATCTGTGCCGGTGGCTCT
GGTCTCTGCTGGGAGCCTTCTTGGCGGTGAGAGGCATCACCTTTCCTGACTTGCTCCCAGCGTGAAATGC
ACCTGCCAAGAATGGCAGACATAGGGACCCCGCCTCCTGGGCCTTCACATGCCCAGTTTTCTTCGGCTCT
GTGGCCTGAAGCGGTCTGTGGACCTTGGAAGTAGGGCTCCAGCACCGACTGGCCTCAGGCCTCTGCCTCA
TTGGTGGTCGGGTAGCGGCCAGTAGGGCGTGGGAGCCTGGCCATCCCTGCCTCCTGGAGTGGACGAGGTT
GGCAGCTGGTCCGTCTGCTCCTGCCCCACTCTCCCCCGCCCCTGCCCTCACCCTACCCTTGCCCCACGCC
TGCCTCATGGCTGGTTGCTCTTGGAGCCTGGTAGTGTCACTGGCTCAGCCTTGCTGGGTATACACAGGCT
CTGCCACCCACTCTGCTCCAAGGGGCTTGCCCTGCCTTGGGCCAAGTTCTAGGTCTGGCCACAGCCACAG
ACAGCTCAGTCCCCTGTGTGGTCATCCTGGCTTCTGCTGGGGGCCCACAGCGCCCCTGGTGCCCCTCCCC
TCCCAGGGCCCGGGTTGAGGCTGGGCCAGGCCCTCTGGGACGGGGACTTGTGCCCTGTCAGGGTTCCCTA
TCCCTGAGGTTGGGGGAGAGCTAGCAGGGCATGCCGCTGGCTGGCCAGGGCTGCAGGGACACTCCCCCTT
TTGTCCAGGGAATACCACACTCGCCCTTCTCTCCAGCGAACACCACACTCGCCCTTCTCTCCAGGGGACG
CCACACTCCCCCTTCTGTCCAGGGGACGCCACACTCCCCCTTCTCTCCAGGGGACGCCACACTCGCCCTT
CTCTCCAGGGGACGCCACACTCGCCCTTCTCTCCAGGGGACGCCACACTCGCCCTTCTGTCCAGGGGACG
CCACACTCGCCCTTCTCTCCAGGGGACGCCACACTCGCCCTTCTCTCCAGGGGACGCCACACTCCCCCTT
CTGTCCAGGGGACGCCACACTCCCCCTTCTCTCCAGGGGACGCCACACTCCCCCTTCTCTCCAGGGGACG
CCACACTCGCCCTTCTCTCCAGGGGACGCCACACTCCCCCTTCTGTCCAGGGGACGCCACACTCGCCCTT
CTCTCCAGGGGACGCCACACTCGCCCTTCTCTCCAGGGGACGCCACACTCCCCCTTCTCTCCAGGGGACG
CCACACTCCCCCTTCTCTCCAGGGGACGCCACACTCCCCCTTCTGTCCAGGGGACGCCACACTCGCCCTT
CTCTCCAGGGGACGCCACACTCCCCCTTCTCTCCAGGGGACGCCACACTCCCCCTTCTCTCCAGGGGACG
CCACACTCCCCCTTCTGTCCAGGGGACGCCACACTCGCCCTTCTCTCCAGGGGACGCCACACTCGCCCTT
CTCTCCAGGGGACGCCACACTCGCCCTTCTCTCCAGGGGACGCCACACTTGCCCTTCTGTCCAGGGAATG
CCACACTCCCCCTTCTCCCCAGCAGCCTCCGAGTGACCAGCTTCCCCATCGATAGACTTCCCGAGGCCAG
GAGCCCTCTAGGGCTGCCGGGTGCCACCCTGGCTCCTTCCACACCGTGCTGGTCACTGCCTGCTGGGGGC
GTCAGATGCAGGTGACCCTGTGCAGGAGGTATCTCTGGACCTGCCTCTTGGTCATTACGGGGCTGGGCAG
GGCCTGGTATCAGGGCCCCGCTGGGGTTGCAGGGCTGGGCCTGTGCTGTGGTCCTGGGGTGTCCAGGACA
GACGTGGAGGGGTCAGGGCCCAGCACCCCTGCTCCATGCTGAACTGTGGGAAGCATCCAGGTCCCTGGGT
GGCTTCAACAGGAGTTCCAGCACGGGAACCACTGGACAACCTGGGGTGTGTCCTGATCTGGGGACAGGCC
AGCCACACCCCGAGTCCTAGGGACTCCAGAGAGCAGCCCACTGCCCTGGGCTCCACGGAAGCCCCCTCAT
GCCGCTAGGCCTTGGCCTCGGGGACAGCCCAGCTAGGCCAGTGTGTGGCAGGACCAGGCCCCCATGTGGG
AGCTGACCCCTTGGGATTCTGGAGCTGTGCTGATGGGCAGGGGAGAGCCAGCTCCTCCCCTTGAGGGAGG
GTCTTGATGCCTGGGGTTACCCGCAGAGGCCTGGGTGCCGGGACGCTCCCCGGTTTGGCTGAAAGGAAAG
CAGATGTGGTCAGCTTCTCCACTGAGCCCATCTGGTCTTCCCGGGGCTGGGCCCCATAGATCTGGGTCCC
TGTGTGGCCCCCCTGGTCTGATGCCGAGGATACCCCTGCAAACTGCCAATCCCAGAGGACAAGACTGGGA
AGTCCCTGCAGGGAGAGCCCATCCCCGCACCCTGACCCACAAGAGGGACTCCTGCTGCCCACCAGGCATC
CCTCCAGGGATCC

Splice Site Prediction

V00574 (see above)

>test1 Human 5' and 3' splice site Test Sequence
aataatagctgtttctctgttgtttaaaggcactacaaatactgtggcagcatataatttcccaggtggccggcgcttcaggtgagtggcaccagcccctggaagcccgg