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Table 5 Mammalian genes corresponding to sequenced cDNA clones

From: Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence

  Genes corresponding to sequenced cDNA clones   Sequenced cDNA clones containing full-length CDSs
  Unique Gene ID (without HomoloGene ID) Unique HomoloGene ID   Unmapped cDNA clones   cDNA clones(with corresponding loci on pig genome) Unique Gene ID (with corresponding loci on pig genome) Loci with Gene ID Gene ID with cDNA clones unmapped on pig genomea
   Unique Gene ID (without Homolo Gene ID) Unique HomoloGene ID  
Human 11,298  (397) 10,889   604  (31) 572   12,498  (11,904) 5966  (5509) 5749 276
Mouse 10,688  (444) 10,197   553  (37) 513   12,354  (11,762) 5597  (5365) 5567 269
Cattle 10,881  (1329) 9487   568  (88) 479   12,622  (12,045) 5667  (5435) 5622 270
Dog 10,082  (469) 9556   522  (28) 492   9642  (9150) 4188  (4011) 4200 208
Pig 10,752     342     11,873  (11,420) 5244  (5116) 5343 182
Totalb          14,616  (13,962)    6466  
  1. Numbers of genes that had unique NCBI Gene IDs and corresponded to the sequences of the pig cDNA clones are shown at the left side of the table. Also shown are the numbers that had unique Gene IDs in the NCBI HomoloGene database (a database of orthologs among species) and corresponded to the sequences of pig cDNA clones. The numbers of unique Gene IDs corresponding to sequences of pig cDNA clones that were not mapped at any locations on the draft pig genome sequence (Sscrofa10.2) are also shown. In addition, the numbers of genes that had unique Gene IDs in the NCBI HomoloGene database and corresponded to the sequences of the unmapped pig cDNA clones are indicated. Numbers in parentheses indicate numbers of unique Gene IDs that had no corresponding HomoloGene IDs. Numbers of HomoloGene IDs in pigs are not indicated, because there is no HomoloGene ID database for pig genes. At the right side of the table, The numbers of cDNA clones estimated to contain full-length coding sequences (CDSs) of pig genes by alignment against the protein sequences of humans, mice, cattle, and dogs in the NCBI RefSeq database are shown in the first column. Pig protein sequences registered in RefSeq were used in this analysis. The numbers of unique NCBI Gene IDs corresponding to the cDNA clones and the numbers of loci corresponding to the cDNA clones examined using the draft sequence of the pig genome (Sscrofa10.2) are also indicated (“Loci with Gene ID”).
  2. a We counted the unique NCBI Gene IDs corresponding to cDNA clones that were not mapped on the draft sequence of the pig genome. If the Gene IDs corresponded to cDNA clones both mapped on, and not mapped on, the draft genome sequence, they were counted in both the “Loci with Gene ID” column and the “Gene ID with cDNA unmapped on pig genome” column.
  3. b Redundant cDNA clones corresponding to genes of more than one species were counted without repetition.