Cut the contig (39951bp) into three parts with some overlaps Fragment 1: 1-14000 Fragment 2: 12001-26000 Fragment 3: 24001-39951 Repeats found with Dotplot analysis Clustalw result of the repeat sequence GCG graphics result of the repeat sequence
No Start-end Start-end Start-end Start-end Start-end Repaet1 14-49 51-229 231-278 280-334 336-475 Repeat2 12393-12428 12430-12608 12610-12657 12659-12713 12715-12854 Repeat3 23080-23115 23117-23295 23297-23344 23346-23400 23402-23541 Length 36 179 48 55 140 Sequence CCATGG-TATACA ACTGTC-TTCACA TAGTGC-TCTTGT TCCAGG-CATCGT GTAGCC-GATGGG Dived the sequence into 3 parts: MDR1: 1-12390 MDR3: 12371-23075 FRAG3: 23061-39951 Align MDR1_HUMAN N and C terminal to determine domains in MDR1 MDR1N_HUMAN: 1-666 (666 AA) MDR1C_HUMAN: 667-1280 (614 AA) Retrive MDR1 and MDR3 AA sequence from SWISSPROT
Code No AA Oganism MDR1_HUMAN 1280 Human MDR1_LEIEN 1280 Leshmania enriettii MDR1_MOUSE 1276 Mouse MDR1_RAT 1277 Rat MDR1_CRIGR 1276 Chinese hamster MDR1_CAEEL 1321 C. elegans MDR3_HUMAN 1279 Human MDR3_MOUSE 1276 Mouse MDR3_CRIGR 1281 Chinese Hamster MDR3_CAEEL 1254 C. elegans Multiple sequence alignment - WebGene output AA sequence allignment to find best conserved fragments in MDR1 and MDR3 gene Alignment 1 - Based on fragment 1-12390 and 12371-23075 Alignment 2 - Based on fragment 1-14000 and 12000-26000 together with 1-12390 and 12371-23075 Alignment 3 - Based on Gene_Finder FGenesH for fragment 1-14000 and 12000-26000 Alignment 4 - Edited Gene_finder FGenesH result Problems in gene1: the 1st exon of both N and C terminal subunit was missed!
Gene 2 analysis Alignment of gene 2 aa sequence with human MDR1 and MDR 3 All 28 exons in gene 2 were icked up! C elegans MDR exons has different structure (NEW!!!)exon 12 was wrong in Gene finder output exon 13 was mixed in exon 12 in Gene Finder output Intron 12 was mannualy picked up with Staden Exon 26 was picked up manually (to be checked) Extra base problem Email to Yu Jun Gene 2 cDNA sequnece with translation Gene 2 amino acid sequnece Alignment of gene 2 cDNA with human MDR3 DNA Alignment of gene 2 amino acis with human MDR3 DNA Based on FgenH output, we can assign the 2 MDR genes. No TSS Exon-S Exon-E PolyA Gene-S Gene-E Gene-L ----------------------------------------------------------- 0 980 1000 1 2279 2667 12870 13091 2279 13105 10827 2 13221 13741 23557 23696 13221 23710 10490Gene 1 analysis Some exons are missed in gene 1 prediction exon comparison of human and fugu Local aliangment of gene 1 and gene 2 DNA sequence Global aliangment of gene 1 and gene 2 DNA sequence Gene 2 exon numbering based on the original contig sequence
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Last modified: Sat, 21 Aug 1999, [email protected]
