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Table 1 Exemplificative zebrafish genes with extended cDNA 5' region and deduced protein.

From: Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach

Gene (RefSeq#)

Error typea

GenBank EST# Zebrafishb

Genomic clone #

Product length new/old (no. of new amino acids)

Kozak sequence old (top)/new (bottom). Consensec: GCCR CCATGG

GenBank EST# Non-zebrafish

selt1a (NM_178290)

ND

CN505709

-

196/163 (33, +20%)

ATGA AGATG C

-

  

CK681469

  

CTGA TCATG G

 
  

CN018643d

    

unc119.2 (NM_205713)

1

CN505408

BX465229

264/206 (58, +28%)

GAGG CCATG A

pp DT261717e

  

CK363344

BX005137

 

CGGA TAATG A

pp DT134309

  

BI710727d

   

pp DT116366

      

pp DT263287

nppa (NM_198800)

1, 2

CN176149

BX323876

139/106 (33, +31%)

AGCA ACATG G

-

  

CN180261

  

TCAG AGATG G

 
  

CO929886d

    
  1. a (1) extended exon 1; (2) new exon; ND: not determined owing to unavailability of genomic sequence.
  2. b GenBank sequences matching extended coding sequence from the new start codon in EST (Expressed Sequence Tag) division.
  3. c The two most conserved positions (Kozak, 1999; Kozak, 2002) are underlined; start codon, in bold font.
  4. d Only three representative sequences are listed, out of a total of 24 for selt1a, 4 for unc119.2, and 26 for nppa, showing consistent coding sequence extension (see Table online).
  5. e pp = Pimephales promelas fish.