Skip to main content

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.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us