RefSeq mRNAs mapped to this assembly (NM_001193337)
Item: NM_001193337
Score: 0
Position: NC_044213.2:49567536-50587804
Genomic Size: 1020269
Strand: -
View DNA for this feature (GCF_003957565.2/zebra finch (v1.4 2021))

Alternative/human readable name
Status of CDS start annotation (none, unknown, incomplete, or complete)none
Status of CDS end annotation (none, unknown, incomplete, or complete)none
Exon frame {0,1,2}, or -1 if no frame for exon-1,-1,-1,-1,-1,-1,1,1,1,0,1,1,0,1,1,2,1,1,1,1,2,2,2,1,0,0,2,1,1,1,0,-1,-1,-1,
Transcript type
gene nameCNTNAP2
species of origin of the mRNATaeniopygia guttata
Gene type

Links to sequence:

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The RefSeq mRNAs gene track for the 04 May 2021 Taeniopygia guttata/GCF_003957565.2_bTaeGut1.4.pri genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 1,056,271,262
Gene count: 12,747
Bases in genes: 399,271,120
Percent genome coverage: % 37.800

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The mRNAs were aligned against the Taeniopygia guttata/GCF_003957565.2_bTaeGut1.4.pri genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept.

Specifically, the translated blat command is:

blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl

where target.fa is one of the chromosome sequence of the genome assembly,
and the query.fa is the mRNAs from RefSeq
The resulting PSL outputs are filtered:
pslCDnaFilter -minId=0.35 -minCover=0.25  -globalNearBest=0.0100 -minQSize=20 
  -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap 
    all.results.psl GCF_003957565.2_bTaeGut1.4.pri.xenoRefGene.psl
The filtered GCF_003957565.2_bTaeGut1.4.pri.xenoRefGene.psl is converted to genePred data to display for this track.


The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.


Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518