RIC7 sequence identity and experimental primer mapping

Analysis date: 2026-09-07. Reproduction instructions and input provenance.
Computed output: results.json. Coordinates below are 1-based,
inclusive, on the supplied transcript sequence.

Finding

The published RIC7 primer pairs from Wu et al. (2001), Hong et al.
(online 2015/issue 2016), and Zhu et al. (2021) map to the AT4G28556 transcript NM_001036663.2,
which encodes the CRIB protein Q1G3K8. None of the six primers has an exact
3′ match of 14 or more bases in the AT4G28560 transcript NM_118998.1.
The comparison strongly assigns these experimental targets to the CRIB locus.
It is a comparison of the two candidate loci, not a genome-wide specificity test.

Sequence identity

Sequence	Comparator	Result
F4JLB7	NP_194585.1	Exact equality, 450 aa
F4JLB7	Translation of NC_003075.7 reverse interval 14116015–14117367	Exact equality, 450 aa
Q1G3K8	NP_001031740.1	Exact equality, 216 aa
Q1G3K8	DQ487576.1 annotated CDS translation	Exact equality, 216 aa

Primer mapping

Primer	Matched bases	Removed 5′ bases	NM_001036663.2 match
Wu2001 RIC7 forward	21	7	660–680
Wu2001 RIC7 reverse	23	0	1281–1303, reverse complement
Hong2016 RIC7 forward	29	0	705–733
Hong2016 RIC7 reverse	29	0	1256–1284, reverse complement
Zhu2021 RIC7 forward	22	0	804–825
Zhu2021 RIC7 reverse	22	0	917–938, reverse complement

Primer sequences and source URLs are in data/primers.tsv:
Wu et al., Table 4, DOI:10.1105/tpc.010218
and Hong et al., RT-PCR methods, DOI:10.1111/nph.13625.
Forward and reverse matches have the expected inward-facing orientation. Each
primer has one longest-suffix hit on this transcript. The Wu forward primer's
removed 5′ sequence contains a BamHI cloning site.

The four Wu/Hong primers also match the cDNA DQ487576.1: forward/reverse positions
10–30 and 631–651 for Wu, and 55–83 and 606–634 for Hong. The Wu reverse
primer matches 21 bases at the cDNA end, requiring two 5′ bases to be discarded;
its entire 23 bases match the longer RefSeq transcript. No matching hits were
found in NM_118998.1 under the same rules.

The Wu forward primer matches near, rather than exactly at, the start of the
current Q1G3K8 CDS. These results identify the locus but do not establish that
the original fusion expressed exactly the current 216-residue protein. Hong's
primers are transcript-assay primers; they do not independently sequence every
expression construct, promoter fragment, or mutant insertion.

Verification checklist

[x] The analysis code reads sequences, primer sequences, directions and comparison pairs from input files; it contains no hardcoded biological conclusions or expected matches.
[x] The same matching code was run on a separate biological input, the AT4G28560 transcript, as well as the AT4G28556 transcript and DQ487576 cDNA.
[x] Synthetic forward, reverse-complement, 5′-tail, multiple-occurrence and no-hit checks passed.
[x] All comparisons completed; direct machine-readable results are retained.
[x] Input sources, sequence versions, methods, dependency version and limitations are documented.
Original physical clones, promoter fragments and insertion sites were not resequenced or fully reconstructed; these are outside the scope of the sequence comparison.

The Zhu et al. (2021) qRT-PCR primers match DQ487576.1 at 154–175
and 267–288 respectively (all 22 bases each), with no hits in NM_118998.1.
The methods were read in cached full text
PMID:33586611(https://doi.org/10.1080/15592324.2021.1876379).