The refSeq are located in the table refGene
of the UCSC mysql server. The field name2
can be used to get all the transcripts for the same gene.
mysql -h genome-mysql.cse.ucsc.edu -A -u genome -D hg18
mysql> select * from refGene as G where chrom="chr1" and txStart > 1000000 and txEnd < 2000000 limit 2\G
*************************** 1. row ***************************
bin: 592
name: NM_017891
chrom: chr1
strand: -
txStart: 1007060
txEnd: 1041599
cdsStart: 1008135
cdsEnd: 1016786
exonCount: 10
exonStarts: 1007060,1009595,1009723,1011120,1012381,1012744,1015595,1016714,1017233,1041302,
exonEnds: 1008230,1009626,1009749,1011255,1012447,1012840,1015671,1016808,1017346,1041599,
id: 0
name2: C1orf159
cdsStartStat: cmpl
cdsEndStat: cmpl
exonFrames: 1,0,1,1,1,1,0,0,-1,-1,
*************************** 2. row ***************************
bin: 593
name: NR_029639
chrom: chr1
strand: +
txStart: 1092346
txEnd: 1092441
cdsStart: 1092441
cdsEnd: 1092441
exonCount: 1
exonStarts: 1092346,
exonEnds: 1092441,
id: 0
name2: MIR200B
cdsStartStat: unk
cdsEndStat: unk
exonFrames: -1,
2 rows in set (0.20 sec)
It can be downloaded here
The file suggested by Pierre could be uploaded to GALAXY. A second file containing your gene/loci of interest can be used to pull out 'join' all the corresponding RefSeq transcripts using 'Join, Subtract and Group' > 'Join two Queries'