Phosphatase GeneID SpurP128
SpurP128 is a fragment of true gene or redundant to SpurP128?
1. BLAT the protein sequences of SpurP128 and SpurP129 in UCSC Genome Browser. The results showed SpurP128 is encoded by Scaffold44006 and SpurP129 by Scaffold68504.
browser details SpurP128 120 1 40 40 100.0% Scaffold68504 +- 16322 16441 120
browser details SpurP128 120 1 40 40 100.0% Scaffold44006 +- 679 798 120
browser details SpurP129 456 40 192 192 100.0% Scaffold68504 +- 15290 23479 8190
browser details SpurP129 120 1 42 192 97.7% Scaffold16437 +- 1554 1679 126
browser details SpurP129 114 102 139 192 100.0% Scaffold44006 +- 679 792 114
2. We then retrieved the genomic sequence encoding SpurP128 and BLATed it. There is a single bp difference in the alignment between the genomic sequence encoding SpurP128 and SpurP129. So, is it an allelic sequence?
browser details strPur2_dna 120 1 120 120 100.0% Scaffold44006 + 679 798 120
browser details strPur2_dna 118 1 120 120 99.2% Scaffold68504 + 16322 16441 120
3. We then retrieved the genomic sequence encoding SpurP128 with flanking regions, the full sequence of Scaffold44006, which is only 868 bp long (see below). We BLATed the sequence and found it aligned to Scaffold68504 (encoding SpurP129) with a high coverage and 89.9% sequence identity, which indicated SpurP128 and SpurP129 are two different genes. Below are the BLAT results:
browser details strPur2_dna 868 1 868 868 100.0% Scaffold44006 + 1 868 868
browser details strPur2_dna 353 1 846 868 89.9% Scaffold68504 + 15826 16490 665
>strPur2_dna range=Scaffold44006:1-868 5'pad=0 3'pad=0 strand=+ repeatMasking=none
TTTTACAAGAAAAAGATGTTTTTCTATCCAATATTCTGACTACCTTAGCA
ATGTTGTTTGTCTACTATCTTTCATCAGGCTATGAATGATTATTCTCAAT
ACATATATGGCTTTACGTGAAGTCCTTAAGCACATAAGTGAATGTTATTC
ATCCCTATTCTCTACTTCACTCGGTGTAGAGTGTTCCTACCATATGGCCT
CTATGAGAGCTTATAACAGTTCTAGAACCTAGCGAGTCATGTGTAAAACC
CATTGCCCTTTAATTGTTGTTTAAAGGAGCTCCATTTACCTATTGTAAAG
GTAAAGTTCCTGTCTTGTTATTTCAAAATGTTTCTTCTCTGTTTTACGGC
TACCCCTCTTGAGCTTAAATTACTCTCTGGTTCAGTAAAATTCTCCACAT
TTTACAGTCAAATTTGAAATTATTCTCAGATGAACTTTCCCTAGTTTCAA
TGAGACTTAATCAAAACCTTAAAATCACAAATTGACAGTGCCTGGGTACA
AGGGACAATCACATAATTGAACTCTCCAAATCAAATTCATAGCTGCATGT
ATTAAACGGTAAGAATGCTTTCGTCGCCTAGTAGTAAAAATGACTCGCGC
ATCTTCTGCATCAACTCTCCTGAACTTTGAGAAAGATTTGTCAGAGACGA
ATTATAATTTCAGCGCCCTCAACGTACCTGGAAAGAGCCTGTATGCACCG
GGTGAGTTATCCACAATGAATATACTAGAGAGATCTGGATGTACTGCAGA
TAAATCCTTTGTGTAGCTCCCTGAGTCTAGTGTGCAATGCTGCAGGAAAC
CAGAGGATTGATAGACATAAGAAATTATTGAATAATAGATCATTTAGATG
CTGGTATACAGTAGGCTT
