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Slot: first ribosomal sequence (isolate_ribosomal_seq)

Primary ribosomal sequence for strain verification. For microbial drafts must be >1300 nt; for single cells >220 bp with <10% Ns. Use only A, C, G, T, or N with no FASTA header line.

URI: nmdc_sub_schema:isolate_ribosomal_seq Alias: isolate_ribosomal_seq

Applicable Classes

Name Description Modifies Slot
JgiIsolateGenomeInterface JGI submission metadata for isolate GENOME sequencing projects yes

Properties

  • Range: String

  • Required: True

  • Regex pattern: ^[ATCGN]{200,5000}$

Aliases

  • First ribosomal sequence

Examples

Value
AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACT

Comments

  • Required for all microbial and fungal genome projects.
  • 16S is required for microbial drafts and single cells; ITS for fungal drafts.
  • Sequence must come from the actual sample to be shipped to JGI.

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc_sub_schema:isolate_ribosomal_seq
native nmdc_sub_schema:isolate_ribosomal_seq

LinkML Source

name: isolate_ribosomal_seq
description: Primary ribosomal sequence for strain verification. For microbial drafts
  must be >1300 nt; for single cells >220 bp with <10% Ns. Use only A, C, G, T, or
  N with no FASTA header line.
title: first ribosomal sequence
comments:
- Required for all microbial and fungal genome projects.
- 16S is required for microbial drafts and single cells; ITS for fungal drafts.
- Sequence must come from the actual sample to be shipped to JGI.
examples:
- value: AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACT
from_schema: https://example.com/nmdc_submission_schema
aliases:
- First ribosomal sequence
rank: 32
alias: isolate_ribosomal_seq
domain_of:
- JgiIsolateGenomeInterface
range: string
required: true
pattern: ^[ATCGN]{200,5000}$